Isolated polynucleotides and polypeptides, and methods of using same for increasing yield of plants

ABSTRACT

Provided are isolated polynucleotides and nucleic acid constructs which comprise a nucleic acid sequence at least 80% identical to a nucleic acid sequence selected form the group consisting of SEQ ID NOs: 1-219, 367-5628, 9688-9700, and 9709-9752; and isolated polypeptides which comprise an amino acid sequence at least 80% homologous to an amino acid sequence selected from the group consisting of SEQ ID NOs: 220-366, 5629-9400, 9701-9708, and 9753-9796. Also provided are transgenic cells and plants expressing same and methods of using same for increasing yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of a plant.

RELATED APPLICATIONS

This application is a division of U.S. patent application Ser. No.14/368,556 filed on Jun. 25, 2014, which is a National Phase of PCTPatent Application No. PCT/IL2012/050554 having International FilingDate of Dec. 26, 2012, which claims the benefit of priority under 35 USC§ 119(e) of U.S. Provisional Patent Application Nos. 61/603,322 filed onFeb. 26, 2012 and 61/580,674 filed on Dec. 28, 2011. The contents of theabove applications are all incorporated by reference as if fully setforth herein in their entirety.

SEQUENCE LISTING STATEMENT

The ASCII file, entitled 76362SequenceListing.txt. created on Jan. 8,2019, comprising 17,233,155 bytes, submitted concurrently with thefiling of this application is incorporated herein by reference.

FIELD AND BACKGROUND OF THE INVENTION

The present invention, in some embodiments thereof, relates to novelpolynucleotides and polypeptides which can be used to increase yield(e.g., seed/grain yield, oil yield), nitrogen use efficiency, fertilizeruse efficiency, growth rate, vigor, biomass, oil content, fiber yield,fiber quality and/or length, abiotic stress tolerance and/or water useefficiency of a plant and to generate transgenic plants with increasedyield, nitrogen use efficiency, growth rate, vigor, biomass, oilcontent, fiber yield, fiber quality and/or length, abiotic stresstolerance and/or water use efficiency as compared to wild type ornon-transformed plants.

Yield is affected by various factors, such as, the number and size ofthe plant organs, plant architecture (for example, the number ofbranches), grains set length, number of filled grains, vigor (e.g.seedling), growth rate, root development, utilization of water,nutrients (e.g., nitrogen) and fertilizers, and stress tolerance.

Crops such as, corn, rice, wheat, canola and soybean account for overhalf of total human caloric intake, whether through direct consumptionof the seeds themselves or through consumption of meat products raisedon processed seeds or forage. Seeds are also a source of sugars,proteins and oils and metabolites used in industrial processes. Theability to increase plant yield, whether through increase dry matteraccumulation rate, modifying cellulose or lignin composition, increasestalk strength, enlarge meristem size, change of plant branchingpattern, erectness of leaves, increase in fertilization efficiency,enhanced seed dry matter accumulation rate, modification of seeddevelopment, enhanced seed filling or by increasing the content of oil,starch or protein in the seeds would have many applications inagricultural and non-agricultural uses such as in the biotechnologicalproduction of pharmaceuticals, antibodies or vaccines.

A common approach to promote plant growth has been, and continues to be,the use of natural as well as synthetic nutrients (fertilizers). Thus,fertilizers are the fuel behind the “green revolution”, directlyresponsible for the exceptional increase in crop yields during the last40 years, and are considered the number one overhead expense inagriculture. Of the three macronutrients provided as main fertilizers[Nitrogen (N), Phosphate (P) and Potassium (K)], nitrogen is often therate-limiting element in plant growth and all field crops have afundamental dependence on inorganic nitrogenous fertilizer. Nitrogenusually needs to be replenished every year, particularly for cereals,which comprise more than half of the cultivated areas worldwide. Forexample, inorganic nitrogenous fertilizers such as ammonium nitrate,potassium nitrate, or urea, typically accounts for 40% of the costsassociated with crops such as corn and wheat.

Nitrogen is an essential macronutrient for the plant, responsible forbiosynthesis of amino and nucleic acids, prosthetic groups, planthormones, plant chemical defenses, etc. In addition, nitrogen is oftenthe rate-limiting element in plant growth and all field crops have afundamental dependence on inorganic nitrogen. Thus, nitrogen istranslocated to the shoot, where it is stored in the leaves and stalkduring the rapid step of plant development and up until flowering. Incorn for example, plants accumulate the bulk of their organic nitrogenduring the period of grain germination, and until flowering. Oncefertilization of the plant has occurred, grains begin to form and becomethe main sink of plant nitrogen. The stored nitrogen can be thenredistributed from the leaves and stalk that served as storagecompartments until grain formation.

Since fertilizer is rapidly depleted from most soil types, it must besupplied to growing crops two or three times during the growing season.In addition, the low nitrogen use efficiency (NUE) of the main crops(e.g., in the range of only 30-70%) negatively affects the inputexpenses for the farmer, due to the excess fertilizer applied. Moreover,the over and inefficient use of fertilizers are major factorsresponsible for environmental problems such as eutrophication ofgroundwater, lakes, rivers and seas, nitrate pollution in drinking waterwhich can cause methemoglobinemia, phosphate pollution, atmosphericpollution and the like. However, in spite of the negative impact offertilizers on the environment, and the limits on fertilizer use, whichhave been legislated in several countries, the use of fertilizers isexpected to increase in order to support food and fiber production forrapid population growth on limited land resources. For example, it hasbeen estimated that by 2050, more than 150 million tons of nitrogenousfertilizer will be used worldwide annually.

Increased use efficiency of nitrogen by plants should enable crops to becultivated with lower fertilizer input, or alternatively to becultivated on soils of poorer quality and would therefore havesignificant economic impact in both developed and developingagricultural systems.

Genetic improvement of fertilizer use efficiency (FUE) in plants can begenerated either via traditional breeding or via genetic engineering.

Attempts to generate plants with increased FUE have been described inU.S. Pat. Appl. No. 20020046419 to Choo. et al.; U.S. Pat. Appl. No.2005010879 to Edgerton et al.; U.S. Pat. Appl. No. 20060179511 to Chometet al.; Good, A, et al. 2007 (Engineering nitrogen use efficiency withalanine aminotransferase. Canadian Journal of Botany 85: 252-262); andGood A G et al. 2004 (Trends Plant Sci. 9:597-605).

Yanagisawa et al. (Proc. Natl. Acad. Sci. U.S.A. 2004 101:7833-8)describe Dof1 transgenic plants which exhibit improved growth underlow-nitrogen conditions.

U.S. Pat. No. 6,084,153 to Good et al. discloses the use of a stressresponsive promoter to control the expression of Alanine AmineTransferase (AlaAT) and transgenic canola plants with improved droughtand nitrogen deficiency tolerance when compared to control plants.

The ever-increasing world population and the decreasing availability inarable land for agriculture affect the yield of plants and plant-relatedproducts. The global shortage of water supply, desertification, abioticstress (ABS) conditions (e.g., salinity, drought, flood, suboptimaltemperature and toxic chemical pollution), and/or limited nitrogen andfertilizer sources cause substantial damage to agricultural plants suchas major alterations in the plant metabolism, cell death, and decreasesin plant growth and crop productivity.

Drought is a gradual phenomenon, which involves periods of abnormallydry weather that persists long enough to produce serious hydrologicimbalances such as crop damage, water supply shortage and increasedsusceptibility to various diseases.

Salinity, high salt levels, affects one in five hectares of irrigatedland. None of the top five food crops. i.e., wheat, corn, rice,potatoes, and soybean, can tolerate excessive salt. Detrimental effectsof salt on plants result from both water deficit, which leads to osmoticstress (similar to drought stress), and the effect of excess sodium ionson critical biochemical processes. As with freezing and drought, highsalt causes water deficit; and the presence of high salt makes itdifficult for plant roots to extract water from their environment. Thus,salination of soils that are used for agricultural production is asignificant and increasing problem in regions that rely heavily onagriculture, and is worsen by over-utilization, over-fertilization andwater shortage, typically caused by climatic change and the demands ofincreasing population.

Suboptimal temperatures affect plant growth and development through thewhole plant life cycle. Thus, low temperatures reduce germination rateand high temperatures result in leaf necrosis. In addition, matureplants that are exposed to excess of heat may experience heat shock,which may arise in various organs, including leaves and particularlyfruit, when transpiration is insufficient to overcome heat stress. Heatalso damages cellular structures, including organelles and cytoskeleton,and impairs membrane function. Heat shock may produce a decrease inoverall protein synthesis, accompanied by expression of heat shockproteins, e.g., chaperones, which are involved in refolding proteinsdenatured by heat. High-temperature damage to pollen almost alwaysoccurs in conjunction with drought stress, and rarely occurs underwell-watered conditions. Combined stress can alter plant metabolism innovel ways. Excessive chilling conditions, e.g., low, but abovefreezing, temperatures affect crops of tropical origins, such assoybean, rice, maize, and cotton. Typical chilling damage includeswilting, necrosis, chlorosis or leakage of ions from cell membranes.Excessive light conditions, which occur under clear atmosphericconditions subsequent to cold late summer/autumn nights, can lead tophotoinhibition of photosynthesis (disruption of photosynthesis). Inaddition, chilling may lead to yield losses and lower product qualitythrough the delayed ripening of maize.

Nutrient deficiencies cause adaptations of the root architecture,particularly notably for example is the root proliferation withinnutrient rich patches to increase nutrient uptake. Nutrient deficienciescause also the activation of plant metabolic pathways which maximize theabsorption, assimilation and distribution processes such as byactivating architectural changes. Engineering the expression of thetriggered genes may cause the plant to exhibit the architectural changesand enhanced metabolism also under other conditions.

In addition, it is widely known that the plants usually respond to waterdeficiency by creating a deeper root system that allows access tomoisture located in deeper soil layers. Triggering this effect willallow the plants to access nutrients and water located in deeper soilhorizons particularly those readily dissolved in water like nitrates.

Studies have shown that plant adaptations to adverse environmentalconditions are complex genetic traits with polygenic nature.Conventional means for crop and horticultural improvements utilizeselective breeding techniques to identify plants having desirablecharacteristics. However, selective breeding is tedious, time consumingand has an unpredictable outcome. Furthermore, limited germplasmresources for yield improvement and incompatibility in crosses betweendistantly related plant species represent significant problemsencountered in conventional breeding. Advances in genetic engineeringhave allowed mankind to modify the germplasm of plants by expression ofgenes-of-interest in plants. Such a technology has the capacity togenerate crops or plants with improved economic, agronomic orhorticultural traits.

Wheat (Triticum spp) is the most widely grown crop and providesone-fifth of the total calories of the world's population. Future wheatimprovement is expected to meet the considerable challenge of increasingproduction to feed an estimated world population of 9 billion by 2050coupled with the threat of climate change to crop productivity. Sincethe 1960s, increases in productivity have been achieved as a result ofwide-scale adoption of Green Revolution technologies). These hadprincipally been attained by diverting assimilates previously used forlong stem growth to increased size of the grain bearing ears. Thus, postgreen-revolution wheat lines have shorter stature that is associatedwith higher harvest index. However, the wheat harvest index is nowapproaching a plateau and further large increases in harvest index areunlikely to be achieved based only on the breeding approach.Biotechnology tools such as genetic engineering aimed at theintroduction of novel genetic variance into wheat might offer analternative solution. Furthermore, biotechnological approaches have thepotential to complement breeding by reducing the time taken to producecultivars with improved characteristics. However, despite the tremendouspotential for wheat improvement through biotechnology approaches, thesize and complexity of the wheat genome are challenging obstacles on theway to commercial track of transgenic wheat.

U.S. Pat. No. 7,238,862 (Allison et al.) discloses an improvedtransformation and regeneration system for wheat, for efficient andreliable for production of fertile plants with improved agronomicqualities.

WO publication No. 2004/104162 discloses methods of increasing abioticstress tolerance and/or biomass in plants and plants generated thereby.

WO publication No. 2004/111183 discloses nucleotide sequences forregulating gene expression in plant trichomes and constructs and methodsutilizing same.

WO publication No. 2004/081173 discloses novel plant derived regulatorysequences and constructs and methods of using such sequences fordirecting expression of exogenous polynucleotide sequences in plants.

WO publication No. 2005/121364 discloses polynucleotides andpolypeptides involved in plant fiber development and methods of usingsame for improving fiber quality, yield and/or biomass of a fiberproducing plant.

WO publication No. 2007/049275 discloses isolated polypeptides,polynucleotides encoding same, transgenic plants expressing same andmethods of using same for increasing fertilizer use efficiency, plantabiotic stress tolerance and biomass.

WO publication No. 2007/020638 discloses methods of increasing abioticstress tolerance and/or biomass in plants and plants generated thereby.

WO publication No. 2008/122980 discloses genes constructs and methodsfor increasing oil content, growth rate and biomass of plants.

WO publication No. 2008/075364 discloses polynucleotides involved inplant fiber development and methods of using same.

WO publication No. 2009/083958 discloses methods of increasing water useefficiency, fertilizer use efficiency, biotic/abiotic stress tolerance,yield and biomass in plant and plants generated thereby.

WO publication No. 2009/141824 discloses isolated polynucleotides andmethods using same for increasing plant utility.

WO publication No. 2009/013750 discloses genes, constructs and methodsof increasing abiotic stress tolerance, biomass and/or yield in plantsgenerated thereby.

WO publication No. 2010/020941 discloses methods of increasing nitrogenuse efficiency, abiotic stress tolerance, yield and biomass in plantsand plants generated thereby.

WO publication No. 2010/076756 discloses isolated polynucleotides forincreasing abiotic stress tolerance, yield, biomass, growth rate, vigor,oil content, fiber yield, fiber quality, and/or nitrogen use efficiencyof a plant.

WO2010/100595 publication discloses isolated polynucleotides andpolypeptides, and methods of using same for increasing plant yieldand/or agricultural characteristics.

WO publication No. 2010/049897 discloses isolated polynucleotides andpolypeptides and methods of using same for increasing plant yield,biomass, growth rate, vigor, oil content, abiotic stress tolerance ofplants and nitrogen use efficiency.

WO2010/143138 publication discloses isolated polynucleotides andpolypeptides, and methods of using same for increasing nitrogen useefficiency, fertilizer use efficiency, yield, growth rate, vigor,biomass, oil content, abiotic stress tolerance and/or water useefficiency

WO publication No. 2011/080674 discloses isolated polynucleotides andpolypeptides and methods of using same for increasing plant yield,biomass, growth rate, vigor, oil content, abiotic stress tolerance ofplants and nitrogen use efficiency.

WO2011/015985 publication discloses polynucleotides and polypeptides forincreasing desirable plant qualities.

SUMMARY OF THE INVENTION

According to an aspect of some embodiments of the present inventionthere is provided a method of increasing yield, growth rate, biomass,vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen useefficiency, and/or abiotic stress of a plant, comprising expressingwithin the plant an exogenous polynucleotide comprising a nucleic acidsequence encoding a polypeptide at least 80% identical to SEQ ID NO:220-366, 5629-9399, 9400, 9701-9708, 9753-9795 or 9796, therebyincreasing the yield, growth rate, biomass, vigor, oil content, seedyield, fiber yield, fiber quality, nitrogen use efficiency, and/orabiotic stress of the plant.

According to an aspect of some embodiments of the present inventionthere is provided a method of increasing yield, growth rate, biomass,vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen useefficiency, and/or abiotic stress of a plant, comprising expressingwithin the plant an exogenous polynucleotide comprising a nucleic acidsequence encoding a polypeptide selected from the group consisting ofSEQ ID NOs: 220-366, 5629-9399, 9400, 9701-9708, 9753-9795 and 9796,thereby increasing the yield, growth rate, biomass, vigor, oil content,seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/orabiotic stress of the plant.

According to an aspect of some embodiments of the present inventionthere is provided a method of producing a crop comprising growing a cropof a plant expressing an exogenous polynucleotide comprising a nucleicacid sequence encoding a polypeptide at least 80% homologous to theamino acid sequence selected from the group consisting of SEQ ID NOs:273, 220-272, 274-366, 5629-9400, 9701-9708, 9753-9795 and 9796, whereinsaid plant is derived from a plant selected for increased yield,increased growth rate, increased biomass, increased vigor, increased oilcontent, increased seed yield, increased fiber yield, increased fiberquality, increased nitrogen use efficiency, and/or increased abioticstress tolerance as compared to a control plant, thereby producing thecrop.

According to an aspect of some embodiments of the present inventionthere is provided a method of increasing yield, growth rate, biomass,vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen useefficiency, and/or abiotic stress of a plant, comprising expressingwithin the plant an exogenous polynucleotide comprising a nucleic acidsequence at least 80% identical to SEQ ID NO: 1-219, 367-5627, 5628,9688-9700, 9709-9751 or 9752, thereby increasing the yield, growth rate,biomass, vigor, oil content, seed yield, fiber yield, fiber quality,nitrogen use efficiency, and/or abiotic stress of the plant.

According to an aspect of some embodiments of the present inventionthere is provided a method of increasing yield, growth rate, biomass,vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen useefficiency, and/or abiotic stress of a plant, comprising expressingwithin the plant an exogenous polynucleotide comprising the nucleic acidsequence selected from the group consisting of SEQ ID NOs: 1-219,367-5627, 5628, 9688-9700, 9709-9751 and 9752, thereby increasing theyield, growth rate, biomass, vigor, oil content, seed yield, fiberyield, fiber quality, nitrogen use efficiency, and/or abiotic stress ofthe plant.

According to an aspect of some embodiments of the present inventionthere is provided a method of producing a crop comprising growing a cropof a plant expressing an exogenous polynucleotide which comprises anucleic acid sequence which is at least 80% identical to the nucleicacid sequence selected from the group consisting of SEQ ID NOs:176,1-175, 177-219, 367-5628, 9688-9700, 9709-9751 and 9752, wherein saidplant is derived from a plant selected for increased yield, increasedgrowth rate, increased biomass, increased vigor, increased oil content,increased seed yield, increased fiber yield, increased fiber quality,increased nitrogen use efficiency, and/or increased abiotic stresstolerance as compared to a control plant, thereby producing the crop

According to an aspect of some embodiments of the present inventionthere is provided an isolated polynucleotide comprising a nucleic acidsequence encoding a polypeptide which comprises an amino acid sequenceat least 80% homologous to the amino acid sequence set forth in SEQ IDNO: 220-366, 5629-9399, 9400, 9701-9708, 9753-9795 or 9796, wherein theamino acid sequence is capable of increasing yield, growth rate,biomass, vigor, oil content, seed yield, fiber yield, fiber quality,nitrogen use efficiency, and/or abiotic stress of a plant.

According to an aspect of some embodiments of the present inventionthere is provided an isolated polynucleotide comprising a nucleic acidsequence encoding a polypeptide which comprises the amino acid sequenceselected from the group consisting of SEQ ID NOs: 220-366, 5629-9399,9400, 9701-9708, 9753-9795 and 9796.

According to an aspect of some embodiments of the present inventionthere is provided an isolated polynucleotide comprising a nucleic acidsequence at least 80% identical to SEQ ID NOs: 1-219, 367-5627, 5628,9688-9700, 9709-9751 and 9752, wherein the nucleic acid sequence iscapable of increasing yield, growth rate, biomass, vigor, oil content,seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/orabiotic stress of a plant.

According to an aspect of some embodiments of the present inventionthere is provided an isolated polynucleotide comprising the nucleic acidsequence selected from the group consisting of SEQ ID NOs: 1-219,367-5627, 5628, 9688-9700, 9709-9751 and 9752.

According to an aspect of some embodiments of the present inventionthere is provided a nucleic acid construct comprising the isolatedpolynucleotide of some embodiments of the invention, and a promoter fordirecting transcription of the nucleic acid sequence in a host cell.

According to an aspect of some embodiments of the present inventionthere is provided an isolated polypeptide comprising an amino acidsequence at least 80% homologous to SEQ ID NO: 220-366, 5629-9399, 9400,9701-9708, 9753-9795 or 9796, wherein the amino acid sequence is capableof increasing yield, growth rate, biomass, vigor, oil content, seedyield, fiber yield, fiber quality, nitrogen use efficiency, and/orabiotic stress of a plant.

According to an aspect of some embodiments of the present inventionthere is provided an isolated polypeptide comprising the amino acidsequence selected from the group consisting of SEQ ID NOs: 220-366,5629-9399, 9400, 9701-9708, 9753-9795 and 9796.

According to an aspect of some embodiments of the present inventionthere is provided a plant cell exogenously expressing the polynucleotideof some embodiments of the invention, or the nucleic acid construct ofsome embodiments of the invention.

According to an aspect of some embodiments of the present inventionthere is provided a plant cell exogenously expressing the polypeptide ofsome embodiments of the invention.

According to an aspect of some embodiments of the present inventionthere is provided a transgenic plant comprising the nucleic acidconstruct of some embodiments of the invention or the plant cell of someembodiments of the invention.

According to some embodiments of the invention, the nucleic acidsequence encodes an amino acid sequence selected from the groupconsisting of SEQ ID NOs: 220-366, 5629-9399, 9400, 9701-9708, 9753-9795and 9796.

According to some embodiments of the invention, the nucleic acidsequence is selected from the group consisting of SEQ ID NOs: 1-219,367-5627, 5628, 9688-9700, 9709-9751 and 9752.

According to some embodiments of the invention, the polynucleotideconsists of the nucleic acid sequence selected from the group consistingof SEQ ID NOs: 1-219, 367-5627, 5628, 9688-9700, 9709-9751 and 9752.

According to some embodiments of the invention, the nucleic acidsequence encodes the amino acid sequence selected from the groupconsisting of SEQ ID NOs: 220-366, 5629-9399, 9400, 9701-9708, 9753-9795and 9796.

According to some embodiments of the invention, the plant cell formspart of a plant.

According to some embodiments of the invention, the method furthercomprising growing the plant expressing the exogenous polynucleotideunder the abiotic stress.

According to some embodiments of the invention, the abiotic stress isselected from the group consisting of salinity, osmotic stress, drought,water deprivation, flood, etiolation, low temperature, high temperature,heavy metal toxicity, anaerobiosis, nutrient deficiency, nutrientexcess, atmospheric pollution and UV irradiation.

According to some embodiments of the invention, the yield comprises seedyield or oil yield.

According to some embodiments of the invention, the method furthercomprising growing the plant expressing the exogenous polynucleotideunder nitrogen-limiting conditions.

According to some embodiments of the invention, the promoter isheterologous to the isolated polynucleotide and/or to the host cell.

According to some embodiments of the invention, the plant is wheat.

According to some embodiments of the invention, expressing the exogenouspolynucleotide is performed using a wheat promoter.

According to some embodiments of the invention, the promoter is suitablefor expression in a wheat plant.

According to some embodiments of the invention, the wheat promotercomprises the nucleic acid sequence selected from the group consistingof SEQ ID NOs: 9811, 9806, 9807, 9804, 9805, 9812, 9813, 9809, 9810,9406, 9409, 9407, 9408, 9797, 9418, 9799, 9800, 9801, 9808, and 9803.

According to an aspect of some embodiments of the present inventionthere is provided a method of growing a crop, the method comprisingseeding seeds and/or planting plantlets of a plant transformed with theisolated polynucleotide of some embodiments of the invention, or thenucleic acid construct of some embodiments of the invention, wherein theplant is derived from plants selected for at least one trait selectedfrom the group consisting of: increased nitrogen use efficiency,increased abiotic stress tolerance, increased biomass, increased growthrate, increased vigor, increased yield and increased fiber yield orquality, and increased oil content as compared to a non-transformedplant, thereby growing the crop.

According to some embodiments of the invention, the non-transformedplant is a wild type plant of an identical genetic background.

According to some embodiments of the invention, the non-transformedplant is a wild type plant of the same species.

According to some embodiments of the invention, the non-transformedplant is grown under identical growth conditions.

Unless otherwise defined, all technical and/or scientific terms usedherein have the same meaning as commonly understood by one of ordinaryskill in the art to which the invention pertains. Although methods andmaterials similar or equivalent to those described herein can be used inthe practice or testing of embodiments of the invention, exemplarymethods and/or materials are described below. In case of conflict, thepatent specification, including definitions, will control. In addition,the materials, methods, and examples are illustrative only and are notintended to be necessarily limiting.

BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS

Some embodiments of the invention are herein described, by way ofexample only, with reference to the accompanying drawings. With specificreference now to the drawings in detail, it is stressed that theparticulars shown are by way of example and for purposes of illustrativediscussion of embodiments of the invention. In this regard, thedescription taken with the drawings makes apparent to those skilled inthe art how embodiments of the invention may be practiced.

In the drawings:

FIG. 1 is a schematic illustration of the modified pGI binary plasmidcontaining the new At6669 promoter (SEQ ID NO: 9405) and the GUSintron(pQYN_6669) used for expressing the isolated polynucleotide sequences ofthe invention. RB—T-DNA right border; LB—T-DNA left border; MCS—Multiplecloning site; RE—any restriction enzyme; NOS pro=nopaline synthasepromoter, NPT-II=neomycin phosphotransferase gene; NOS ter=nopalinesynthase terminator: Poly-A signal (polyadenylation signal);GUSintron—the GUS reporter gene (coding sequence and intron).

FIG. 2 is a schematic illustration of the modified pGI binary plasmidcontaining the new At6669 promoter (SEQ ID NO: 9405) (pQFN, pQFNc) usedfor expressing the isolated polynucleotide sequences of the invention.RB—T-DNA right border; LB—T-DNA left border; MCS—Multiple cloning site;RE—any restriction enzyme; NOS pro=nopaline synthase promoter,NPT-II=neomycin phosphotransferase gene: NOS ter=nopaline synthaseterminator, Poly-A signal (polyadenylation signal); GUSintron—the GUSreporter gene (coding sequence and intron). The isolated polynucleotidesequences of the invention were cloned into the MCS of the vector pQFNc.

FIGS. 3A-3F are images depicting visualization of root development oftransgenic plants exogenously expressing the polynucleotide of someembodiments of the invention when grown in transparent agar plates undernormal (FIGS. 3A-3B), osmotic stress (15% PEG; FIGS. 3C-3D) ornitrogen-limiting (FIGS. 3E-3F) conditions. The different transgeneswere grown in transparent agar plates for 17 days (7 days nursery and 10days after transplanting). The plates were photographed every 3-4 daysstarting at day 1 after transplanting. FIG. 3A—An image of a photographof plants taken following 10 after transplanting days on agar plateswhen grown under normal (standard) conditions. FIG. 3B—An image of rootanalysis of the plants shown in FIG. 3A in which the lengths of theroots measured are represented by arrows. FIG. 3C—An image of aphotograph of plants taken following 10 days after transplanting on agarplates, grown under high osmotic (PEG 15%) conditions. FIG. 3D—An imageof root analysis of the plants shown in FIG. 3C in which the lengths ofthe roots measured are represented by arrows. FIG. 3E—An image of aphotograph of plants taken following 10 days after transplanting on agarplates, grown under low nitrogen conditions. FIG. 3F—An image of rootanalysis of the plants shown in FIG. 3E in which the lengths of theroots measured are represented by arrows.

FIG. 4 is a schematic illustration of the modified pGI binary plasmidcontaining the Root Promoter (pQNa_RP; SEQ ID NO: 9417) used forexpressing the isolated polynucleotide sequences of some embodiments ofthe invention. RB—T-DNA right border; LB—T-DNA left border; NOSpro=nopaline synthase promoter; NPT-II=neomycin phosphotransferase gene;NOS ter=nopaline synthase terminator; Poly-A signal (polyadenylationsignal). The isolated polynucleotide sequences according to someembodiments of the invention were cloned into the MCS of the vector.

FIG. 5 is a schematic illustration of the pQYN plasmid (5714 bp).

FIG. 6 is a schematic illustration of the pQFN plasmid (5967 bp).

FIG. 7 is a schematic illustration of the pQFYN plasmid (8004 bp).

FIG. 8 is a schematic illustration of pQXNc plasmid, which is a modifiedpGI binary plasmid used for expressing the isolated polynucleotidesequences of some embodiments of the invention. RB—T-DNA right border;LB—T-DNA left border: NOS pro=nopaline synthase promoter,NPT-II=neomycin phosphotransferase gene; NOS ter=nopaline synthaseterminator, RE=any restriction enzyme: Poly-A signal (polyadenylationsignal); 35S—the 35S promoter (SEQ ID NO: 9401). The isolatedpolynucleotide sequences of some embodiments of the invention werecloned into the MCS (Multiple cloning site) of the vector.

DESCRIPTION OF SPECIFIC EMBODIMENTS OF THE INVENTION

The present invention, in some embodiments thereof, relates to methodsof increasing yield, biomass, vigor, growth rate, oil content, abioticstress tolerance, fertilizer use efficiency (e.g., nitrogen useefficiency), water use efficiency fiber yield and/or quality of a plant,such as a wheat plant and to transgenic plants with increased yield,biomass, vigor, growth rate, oil content, abiotic stress tolerance,fertilizer use efficiency (e.g., nitrogen use efficiency), water useefficiency fiber yield and/or quality as compared to non-transformedplants.

Before explaining at least one embodiment of the invention in detail, itis to be understood that the invention is not necessarily limited in itsapplication to the details set forth in the following description orexemplified by the Examples. The invention is capable of otherembodiments or of being practiced or carried out in various ways.

The present inventors have identified novel polypeptides andpolynucleotides which can be used to increase yield, growth rate,biomass, oil content, vigor, fiber yield, fiber quality, fertilizer useefficiency (e.g., nitrogen use efficiency) and/or abiotic stresstolerance of a plant.

Thus, as shown in the Examples section which follows, the presentinventors have utilized bioinformatics tools to identify polynucleotideswhich enhance yield (e.g., seed yield, oil yield, oil content), growthrate, biomass, vigor, fiber yield, fiber quality, fertilizer useefficiency (e.g., nitrogen use efficiency) and/or abiotic stresstolerance of a plant. Genes which affect the trait-of-interest wereidentified based on expression profiles of genes of several Sorghum,Maize, Barley, Brachypodium, Foxtail Millet, and Soybean accessions,varieties and tissues, homology with genes known to affect thetrait-of-interest and using digital expression profile in specifictissues and conditions (Tables 1-52, Examples 1-11). Homologouspolypeptides and polynucleotides (e.g., orthologous) having the samefunction were also identified (Table 53, Example 12). The identifiedgenes were cloned (Example 13, Table 54) and transformed intoagrobacterium (Example 14) for the generation of transgenic plants(e.g., transgenic Arabidopsis, Brachypodium or wheat plants) transformedwith the identified genes and with their homologues (Examples 15-17).Transgenic plants over-expressing the identified polynucleotides wereevaluated for plant performance in greenhouse (Examples 18 and 19) andtissue culture (Example 20) experiments. Altogether, these resultssuggest the use of the novel polynucleotides and polypeptides of theinvention for increasing yield (including oil yield, seed yield and oilcontent), growth rate, biomass, vigor, fiber yield and/or quality,fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abioticstress tolerance of a plant.

Thus, according to an aspect of some embodiments of the invention, thereis provided method of increasing yield, growth rate, biomass, vigor, oilcontent, seed yield, fertilizer use efficiency (e.g., nitrogen useefficiency), fiber yield, fiber quality, and/or abiotic stress toleranceof a plant, comprising expressing within the plant an exogenouspolynucleotide comprising a nucleic acid sequence encoding a polypeptideat least about 80%, at least about 81%, at least about 82%, at leastabout 83%, at least about 84%, at least about 85%, at least about 86%,at least about 87%, at least about 88%, at least about 89%, at leastabout 90%, at least about 91%, at least about 92%, at least about 93%,at least about 94%, at least about 95%, at least about 96%, at leastabout 97%, at least about 98%, at least about 99%, or more say 100%homologous to the amino acid sequence selected from the group consistingof SEQ ID NOs: 220-366, 5629-9399, 9400, 9701-9708, 9753-9795 and 9796,thereby increasing the yield, growth rate, biomass, vigor, oil content,seed yield, fiber yield, fiber quality, fertilizer use efficiency (e.g.,nitrogen use efficiency) and/or abiotic stress of the plant.

As used herein the phrase “plant yield” refers to the amount (e.g., asdetermined by weight or size) or quantity (numbers) of tissues or organsproduced per plant or per growing season. Hence increased yield couldaffect the economic benefit one can obtain from the plant in a certaingrowing area and/or growing time.

It should be noted that a plant yield can be affected by variousparameters including, but not limited to, plant biomass; plant vigor:growth rate; seed yield; seed or grain quantity; seed or grain quality;oil yield; content of oil, starch and/or protein in harvested organs(e.g., seeds or vegetative parts of the plant); number of flowers(florets) per panicle (expressed as a ratio of number of filled seedsover number of primary panicles); harvest index; number of plants grownper area; number and size of harvested organs per plant and per area;number of plants per growing area (density); number of harvested organsin field; total leaf area; carbon assimilation and carbon partitioning(the distribution/allocation of carbon within the plant); resistance toshade: number of harvestable organs (e.g. seeds), seeds per pod, weightper seed; and modified architecture [such as increase stalk diameter,thickness or improvement of physical properties (e.g. elasticity)].

As used herein the phrase “seed yield” refers to the number or weight ofthe seeds per plant, seeds per pod, or per growing area or to the weightof a single seed, or to the oil extracted per seed. Hence seed yield canbe affected by seed dimensions (e.g., length, width, perimeter, areaand/or volume), number of (filled) seeds and seed filling rate and byseed oil content. Hence increase seed yield per plant could affect theeconomic benefit one can obtain from the plant in a certain growing areaand/or growing time; and increase seed yield per growing area could beachieved by increasing seed yield per plant, and/or by increasing numberof plants grown on the same given area.

The term “seed” (also referred to as “grain” or “kernel”) as used hereinrefers to a small embryonic plant enclosed in a covering called the seedcoat (usually with some stored food), the product of the ripened ovuleof gymnosperm and angiosperm plants which occurs after fertilization andsome growth within the mother plant.

The phrase “oil content” as used herein refers to the amount of lipidsin a given plant organ, either the seeds (seed oil content) or thevegetative portion of the plant (vegetative oil content) and istypically expressed as percentage of dry weight (10% humidity of seeds)or wet weight (for vegetative portion).

It should be noted that oil content is affected by intrinsic oilproduction of a tissue (e.g., seed, vegetative portion), as well as themass or size of the oil-producing tissue per plant or per growth period.

In one embodiment, increase in oil content of the plant can be achievedby increasing the size/mass of a plant's tissue(s) which comprise oilper growth period. Thus, increased oil content of a plant can beachieved by increasing the yield, growth rate, biomass and vigor of theplant.

As used herein the phrase “plant biomass” refers to the amount (e.g.,measured in grams of air-dry tissue) of a tissue produced from the plantin a growing season, which could also determine or affect the plantyield or the yield per growing area. An increase in plant biomass can bein the whole plant or in parts thereof such as aboveground (harvestable)parts, vegetative biomass, roots and seeds.

As used herein the phrase “growth rate” refers to the increase in plantorgan/tissue size per time (can be measured in cm² per day).

As used herein the phrase “plant vigor” refers to the amount (measuredby weight) of tissue produced by the plant in a given time. Henceincreased vigor could determine or affect the plant yield or the yieldper growing time or growing area. In addition, early vigor (seed and/orseedling) results in an improved field stand.

Improving early vigor is an important objective of modern rice breedingprograms in both temperate and tropical rice cultivars. Long roots areimportant for proper soil anchorage in water-seeded rice. Where rice issown directly into flooded fields, and where plants must emerge rapidlythrough water, longer shoots are associated with vigor. Wheredrill-seeding is practiced, longer mesocotyls and coleoptiles areimportant for good seedling emergence. The ability to engineer earlyvigor into plants would be of great importance in agriculture. Forexample, poor early vigor has been a limitation to the introduction ofmaize (Zea mays L.) hybrids based on Corn Belt germplasm in the EuropeanAtlantic.

It should be noted that a plant yield can be determined under stress(e.g., abiotic stress, nitrogen-limiting conditions) and/or non-stress(normal) conditions.

As used herein, the phrase “non-stress conditions” refers to the growthconditions (e.g., water, temperature, light-dark cycles, humidity, saltconcentration, fertilizer concentration in soil, nutrient supply such asnitrogen, phosphorous and/or potassium), that do not significantly gobeyond the everyday climatic and other abiotic conditions that plantsmay encounter, and which allow optimal growth, metabolism, reproductionand/or viability of a plant at any stage in its life cycle (e.g., in acrop plant from seed to a mature plant and back to seed again). Personsskilled in the art are aware of normal soil conditions and climaticconditions for a given plant in a given geographic location. It shouldbe noted that while the non-stress conditions may include some mildvariations from the optimal conditions (which vary from one type/speciesof a plant to another), such variations do not cause the plant to ceasegrowing without the capacity to resume growth.

The phrase “abiotic stress” as used herein refers to any adverse effecton metabolism, growth, reproduction and/or viability of a plant.Accordingly, abiotic stress can be induced by suboptimal environmentalgrowth conditions such as, for example, salinity, water deprivation,flooding, freezing, low or high temperature, heavy metal toxicity,anaerobiosis, nutrient deficiency, atmospheric pollution or UVirradiation. The implications of abiotic stress are discussed in theBackground section.

The phrase “abiotic stress tolerance” as used herein refers to theability of a plant to endure an abiotic stress without suffering asubstantial alteration in metabolism, growth, productivity and/orviability.

Plants are subject to a range of environmental challenges. Several ofthese, including salt stress, general osmotic stress, drought stress andfreezing stress, have the ability to impact whole plant and cellularwater availability. Not surprisingly, then, plant responses to thiscollection of stresses are related. Zhu (2002) Ann. Rev. Plant Biol. 53:247-273 et al. note that “most studies on water stress signaling havefocused on salt stress primarily because plant responses to salt anddrought are closely related and the mechanisms overlap”. Many examplesof similar responses and pathways to this set of stresses have beendocumented. For example, the CBF transcription factors have been shownto condition resistance to salt, freezing and drought (Kasuga et al.(1999) Nature Biotech. 17: 287-291). The Arabidopsis rd29B gene isinduced in response to both salt and dehydration stress, a process thatis mediated largely through an ABA signal transduction process (Uno etal. (2000) Proc. Natl. Acad. Sci. USA 97: 11632-11637), resulting inaltered activity of transcription factors that bind to an upstreamelement within the rd29B promoter. In Mesembryanthemum crystallinum (iceplant). Patharker and Cushman have shown that a calcium-dependentprotein kinase (McCDPK1) is induced by exposure to both drought and saltstresses (Patharker and Cushman (2000) Plant J. 24: 679-691). Thestress-induced kinase was also shown to phosphorylate a transcriptionfactor, presumably altering its activity, although transcript levels ofthe target transcription factor are not altered in response to salt ordrought stress. Similarly. Saijo et al. demonstrated that a ricesalt/drought-induced calmodulin-dependent protein kinase (OsCDPK7)conferred increased salt and drought tolerance to rice whenoverexpressed (Saijo et al. (2000) Plant J. 23: 319-327).

Exposure to dehydration invokes similar survival strategies in plants asdoes freezing stress (see, for example. Yelenosky (1989) Plant Physiol89: 444-451) and drought stress induces freezing tolerance (see, forexample, Siminovitch et al. (1982) Plant Physiol 69: 250-255; and Guy etal. (1992) Planta 188: 265-270). In addition to the induction ofcold-acclimation proteins, strategies that allow plants to survive inlow water conditions may include, for example, reduced surface area, orsurface oil or wax production. In another example increased solutecontent of the plant prevents evaporation and water loss due to heat,drought, salinity, osmoticum, and the like therefore providing a betterplant tolerance to the above stresses.

It will be appreciated that some pathways involved in resistance to onestress (as described above), will also be involved in resistance toother stresses, regulated by the same or homologous genes. Of course,the overall resistance pathways are related, not identical, andtherefore not all genes controlling resistance to one stress willcontrol resistance to the other stresses. Nonetheless, if a geneconditions resistance to one of these stresses, it would be apparent toone skilled in the art to test for resistance to these related stresses.Methods of assessing stress resistance are further provided in theExamples section which follows.

As used herein the phrase “water use efficiency (WUE)” refers to thelevel of organic matter produced per unit of water consumed by theplant, i.e., the dry weight of a plant in relation to the plant's wateruse. e.g., the biomass produced per unit transpiration.

As used herein the phrase “fertilizer use efficiency” refers to themetabolic process(es) which lead to an increase in the plant's yield,biomass, vigor, and growth rate per fertilizer unit applied. Themetabolic process can be the uptake, spread, absorbent, accumulation,relocation (within the plant) and use of one or more of the minerals andorganic moieties absorbed by the plant, such as nitrogen, phosphatesand/or potassium.

As used herein the phrase “fertilizer-limiting conditions” refers togrowth conditions which include a level (e.g., concentration) of afertilizer applied which is below the level needed for normal plantmetabolism, growth, reproduction and/or viability.

As used herein the phrase “nitrogen use efficiency (NUE)” refers to themetabolic process(es) which lead to an increase in the plant's yield,biomass, vigor, and growth rate per nitrogen unit applied. The metabolicprocess can be the uptake, spread, absorbent, accumulation, relocation(within the plant) and use of nitrogen absorbed by the plant.

As used herein the phrase “nitrogen-limiting conditions” refers togrowth conditions which include a level (e.g., concentration) ofnitrogen (e.g., ammonium or nitrate) applied which is below the levelneeded for normal plant metabolism, growth, reproduction and/orviability.

Improved plant NUE and FUE is translated in the field into eitherharvesting similar quantities of yield, while implementing lessfertilizers, or increased yields gained by implementing the same levelsof fertilizers. Thus, improved NUE or FUE has a direct effect on plantyield in the field. Thus, the polynucleotides and polypeptides of someembodiments of the invention positively affect plant yield, seed yield,and plant biomass. In addition, the benefit of improved plant NUE willcertainly improve crop quality and biochemical constituents of the seedsuch as protein yield and oil yield.

It should be noted that improved ABST will confer plants with improvedvigor also under non-stress conditions, resulting in crops havingimproved biomass and/or yield e.g., elongated fibers for the cottonindustry, higher oil content.

The term “fiber” is usually inclusive of thick-walled conducting cellssuch as vessels and tracheids and to fibrillar aggregates of manyindividual fiber cells. Hence, the term “fiber” refers to (a)thick-walled conducting and non-conducting cells of the xylem: (b)fibers of extraxylary origin, including those from phloem, bark, groundtissue, and epidermis; and (c) fibers from stems, leaves, roots, seeds,and flowers or inflorescences (such as those of Sorghum vulgare used inthe manufacture of brushes and brooms).

Example of fiber producing plants, include, but are not limited to,agricultural crops such as cotton, silk cotton tree (Kapok. Ceibapentandra), desert willow, creosote bush, winterfat, balsa, kenaf,roselle, jute, sisal abaca, flax, corn, sugar cane, hemp, ramie, kapok,coir, bamboo, spanish moss and Agave spp. (e.g. sisal).

As used herein the phrase “fiber quality” refers to at least one fiberparameter which is agriculturally desired, or required in the fiberindustry (further described hereinbelow). Examples of such parameters,include but are not limited to, fiber length, fiber strength, fiberfitness, fiber weight per unit length, maturity ratio and uniformity(further described hereinbelow.

Cotton fiber (lint) quality is typically measured according to fiberlength, strength and fineness. Accordingly, the lint quality isconsidered higher when the fiber is longer, stronger and finer.

As used herein the phrase “fiber yield” refers to the amount or quantityof fibers produced from the fiber producing plant.

As used herein the term “increasing” refers to at least about 2%, atleast about 3%, at least about 4%, at least about 5%, at least about10%, at least about 15%, at least about 20%, at least about 30%, atleast about 40%, at least about 50%, at least about 60%, at least about70%, at least about 80%, increase in yield, growth rate, biomass, vigor,oil content, seed yield, fiber yield, fiber quality, nitrogen useefficiency, and/or abiotic stress of a plant as compared to a nativeplant or a wild type plant [i.e., a plant not modified with thebiomolecules (polynucleotide or polypeptides) of the invention, e.g., anon-transformed plant of the same species which is grown under the same(e.g., identical) growth conditions].

The phrase “expressing within the plant an exogenous polynucleotide” asused herein refers to upregulating the expression level of an exogenouspolynucleotide within the plant by introducing the exogenouspolynucleotide into a plant cell or plant and expressing by recombinantmeans, as further described herein below.

As used herein “expressing” refers to expression at the mRNA andoptionally polypeptide level.

As used herein, the phrase “exogenous polynucleotide” refers to aheterologous nucleic acid sequence which may not be naturally expressedwithin the plant (e.g., a nucleic acid sequence from a differentspecies, e.g., a different plant species) or which overexpression in theplant is desired. The exogenous polynucleotide may be introduced intothe plant in a stable or transient manner, so as to produce aribonucleic acid (RNA) molecule and/or a polypeptide molecule. It shouldbe noted that the exogenous polynucleotide may comprise a nucleic acidsequence which is identical or partially homologous to an endogenousnucleic acid sequence of the plant.

The term “endogenous” as used herein refers to any polynucleotide orpolypeptide which is present and/or naturally expressed within a plantor a cell thereof.

According to some embodiments of the invention, the exogenouspolynucleotide of the invention comprises a nucleic acid sequenceencoding a polypeptide having an amino acid sequence at least about 80%,at least about 81%, at least about 82%, at least about 83%, at leastabout 84%, at least about 85%, at least about 86%, at least about 87%,at least about 88%, at least about 89%, at least about 90%, at leastabout 91%, at least about 92%, at least about 93%, at least about 94%,at least about 95%, at least about 96%, at least about 97%, at leastabout 98%, at least about 99%, or more say 100% homologous to the aminoacid sequence selected from the group consisting of SEQ ID NOs: 220-366,5629-9399, 9400, 9701-9708, 9753-9795 and 9796.

Homologous sequences include both orthologous and paralogous sequences.The term “paralogous” relates to gene-duplications within the genome ofa species leading to paralogous genes. The term “orthologous” relates tohomologous genes in different organisms due to ancestral relationship.

One option to identify orthologues in monocot plant species is byperforming a reciprocal blast search. This may be done by a first blastinvolving blasting the sequence-of-interest against any sequencedatabase, such as the publicly available NCBI database which may befound at: Hypertext Transfer Protocol://World Wide Web (dot) ncbi (dot)nlm (dot) nih (dot) gov. If orthologues in rice were sought, thesequence-of-interest would be blasted against, for example, the 28.469full-length cDNA clones from Oryza sativa Nipponbare available at NCBI.The blast results may be filtered. The full-length sequences of eitherthe filtered results or the non-filtered results are then blasted back(second blast) against the sequences of the organism from which thesequence-of-interest is derived. The results of the first and secondblasts are then compared. An orthologue is identified when the sequenceresulting in the highest score (best hit) in the first blast identifiesin the second blast the query sequence (the originalsequence-of-interest) as the best hit. Using the same rational aparalogue (homolog to a gene in the same organism) is found. In case oflarge sequence families, the ClustalW program may be used [HypertextTransfer Protocol://World Wide Web (dot) ebi (dot) ac (dot)uk/Tools/clustalw2/index (dot) html], followed by a neighbor-joiningtree (Hypertext Transfer Protocol://en (dot) Wikipedia(dot)org/wikilNeighbor-joining) which helps visualizing the clustering.

Homology (e.g., percent homology, identity+similarity) can be determinedusing any homology comparison software computing a pairwise sequencealignment.

Identity (e.g., percent homology) can be determined using any homologycomparison software, including for example, the BlastN software of theNational Center of Biotechnology Information (NCBI) such as by usingdefault parameters.

According to some embodiments of the invention, the identity is a globalidentity. i.e., an identity over the entire amino acid or nucleic acidsequences of the invention and not over portions thereof.

According to some embodiments of the invention, the term “homology” or“homologous” refers to identity of two or more nucleic acid sequences;or identity of two or more amino acid sequences; or the identity of anamino acid sequence to one or more nucleic acid sequence.

According to some embodiments of the invention, the homology is a globalhomology, i.e., an homology over the entire amino acid or nucleic acidsequences of the invention and not over portions thereof.

The degree of homology or identity between two or more sequences can bedetermined using various known sequence comparison tools. Following is anon-limiting description of such tools which can be used along with someembodiments of the invention.

Pairwise global alignment was defined by S. B. Needleman and C. D.Wunsch, “A general method applicable to the search of similarities inthe amino acid sequence of two proteins” Journal of Molecular Biology,1970, pages 443-53, volume 48).

For example, when starting from a polypeptide sequence and comparing toother polypeptide sequences, the EMBOSS-6.0.1 Needleman-Wunsch algorithm(available fromhttp://emboss(dot)sourceforge(dot)net/apps/cvs/emboss/apps/needle(dot)html)can be used to find the optimum alignment (including gaps) of twosequences along their entire length—a “Global alignment”. Defaultparameters for Needleman-Wunsch algorithm (EMBOSS-6.0.1) include:gapopen=10; gapextend=0.5; datafile=EBLOSUM62; brief=YES.

According to some embodiments of the invention, the parameters used withthe EMBOSS-6.0.1 tool (for protein-protein comparison) include:gapopen=8; gapextend=2; datafile=EBLOSUM62; brief=YES.

According to some embodiments of the invention, the threshold used todetermine homology using the EMBOSS-6.0.1 Needleman-Wunsch algorithm is80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, 99%, or 100%.

When starting from a polypeptide sequence and comparing topolynucleotide sequences, the OneModel FramePlus algorithm [Halperin,E., Faigler. S, and Gill-More, R. (1999)—FramePlus: aligning DNA toprotein sequences. Bioinformatics, 15, 867-873) (available fromhttp://www(dot)biocceleration(dot)com/Products(dot)html] can be usedwith following default parameters: model=frame+_p2n.model mode=local.

According to some embodiments of the invention, the parameters used withthe OneModel FramePlus algorithm are model=frame+_p2n.model,mode=qglobal.

According to some embodiments of the invention, the threshold used todetermine homology using the OneModel FramePlus algorithm is 80%, 81%,82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%,96%, 97%, 98%, 99%, or 100%.

When starting with a polynucleotide sequence and comparing to otherpolynucleotide sequences the EMBOSS-6.0.1 Needleman-Wunsch algorithm(available fromhttp://emboss(dot)sourceforge(dot)net/apps/cvs/emboss/apps/needle(dot)html)can be used with the following default parameters: (EMBOSS-6.0.1)gapopen=10; gapextend=0.5; datafile=EDNAFULL; brief=YES.

According to some embodiments of the invention, the parameters used withthe EMBOSS-6.0.1 Needleman-Wunsch algorithm are gapopen=10;gapextend=0.2; datafile=EDNAFULL; brief=YES.

According to some embodiments of the invention, the threshold used todetermine homology using the EMBOSS-6.0.1 Needleman-Wunsch algorithm forcomparison of polynucleotides with polynucleotides is 80%, 81%, 82%,83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,97%, 98%, 99%, or 100%.

According to some embodiment, determination of the degree of homologyfurther requires employing the Smith-Waterman algorithm (forprotein-protein comparison or nucleotide-nucleotide comparison).

Default parameters for GenCore 6.0 Smith-Waterman algorithm include:model=sw.model.

According to some embodiments of the invention, the threshold used todetermine homology using the Smith-Waterman algorithm is 80%, 81%, 82%,83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,97%, 98%, 99%, or 100%.

According to some embodiments of the invention, the global homology isperformed on sequences which are pre-selected by local homology to thepolypeptide or polynucleotide of interest (e.g., 60% identity over 60%of the sequence length), prior to performing the global homology to thepolypeptide or polynucleotide of interest (e.g., 80% global homology onthe entire sequence). For example, homologous sequences are selectedusing the BLAST software with the Blastp and tBlastn algorithms asfilters for the first stage, and the needle (EMBOSS package) or Frame+algorithm alignment for the second stage. Local identity (Blastalignments) is defined with a very permissive cutoff—60% Identity on aspan of 60% of the sequences lengths because it is used only as a filterfor the global alignment stage. In this specific embodiment (when thelocal identity is used), the default filtering of the Blast package isnot utilized (by setting the parameter “-F F”).

In the second stage, homologs are defined based on a global identity ofat least 80% to the core gene polypeptide sequence.

According to some embodiments of the invention, two distinct forms forfinding the optimal global alignment for protein or nucleotide sequencesare used:

1. Between Two Proteins (Following the Blastp Filter):

EMBOSS-6.0.1 Needleman-Wunsch algorithm with the following modifiedparameters: gapopen=8 gapextend=2. The rest of the parameters areunchanged from the default options listed here:

Standard (Mandatory) Qualifiers:

[-asequence] sequence filename and optional format, or reference (inputUSA)

[-bsequence] seqall Sequence(s) filename and optional format, orreference (input USA)

-gapopen float [10.0 for any sequence]. The gap open penalty is thescore taken away when a gap is created. The best value depends on thechoice of comparison matrix. The default value assumes you are using theEBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix fornucleotide sequences. (Floating point number from 1.0 to 100.0)

-gapextend float [0.5 for any sequence]. The gap extension, penalty isadded to the standard gap penalty for each base or residue in the gap.This is how long gaps are penalized. Usually you will expect a few longgaps rather than many short gaps, so the gap extension penalty should belower than the gap penalty. An exception is where one or both sequencesare single reads with possible sequencing errors in which case you wouldexpect many single base gaps. You can get this result by setting the gapopen penalty to zero (or very low) and using the gap extension penaltyto control gap scoring. (Floating point number from 0.0 to 10.0)

[-outfile] align [*.needle] Output alignment file name

Additional (Optional) Qualifiers:

-datafile matrixf [EBLOSUM62 for protein, EDNAFULL for DNA]. This is thescoring matrix file used when comparing sequences. By default it is thefile ‘EBLOSUM62’ (for proteins) or the file ‘EDNAFULL’ (for nucleicsequences). These files are found in the ‘data’ directory of the EMBOSSinstallation.

Advanced (Unprompted) Qualifiers:

[no]brief boolean [Y] Brief identity and similarity

Associated Qualifiers:

“asequence” associated qualifiers sbegin1 integer Start of the sequenceto be used send1 integer End of the sequence to be used sreverse1boolean Reverse (if DNA) sask1 boolean Ask for begin/end/reversesnucleotide1 boolean Sequence is nucleotide sprotein1 boolean Sequenceis protein slower1 boolean Make lower case supper1 boolean Make uppercase sformat1 string Input sequence format sdbname1 string Database namesid1 string Entryname ufo1 string UFO features fformat1 string Featuresformat fopenfile1 string Features file name “bsequence” associatedqualifiers sbegin2 integer Start of each sequence to be used send2integer End of each sequence to be used sreverse2 boolean Reverse (ifDNA) sask2 boolean Ask for begin/end/reverse snucleotide2 booleanSequence is nucleotide sprotein2 boolean Sequence is protein slower2boolean Make lower case supper2 boolean Make upper case sformat2 stringInput sequence format sdbname2 string Database name sid2 stringEntryname ufo2 string UFO features fformat2 string Features formatfopenfile2 string Features file name “outfile” associated qualifiersaformat3 string Alignment format aextension3 string File name extensionadirectory3 string Output directory aname3 string Base file name awidth3integer Alignment width aaccshow3 boolean Show accession number in theheader adesshow3 boolean Show description in the header ausashow3boolean Show the full USA in the alignment aglobal3 boolean Show thefull sequence in alignment

General Qualifiers:

auto boolean Turn off prompts stdout boolean Write first file tostandard output filter boolean Read first file from standard input,write first file to standard output options boolean Prompt for standardand additional values debug boolean Write debug output to program,dbgverbose boolean Report some/full command line options help booleanReport command line options. More information on associated and generalqualifiers can be found with -help -verbose warning boolean Reportwarnings error boolean Report errors fatal boolean Report fatal errorsdie boolean Report dying program messages

2. Between a Protein Sequence and a Nucleotide Sequence (Following theTblastn Filter):

GenCore 6.0 OneModel application utilizing the Frame+algorithm with thefollowing parameters: model=frame+_p2n.modelmode=qglobal−q=protein.sequence -db=nucleotide.sequence. The rest of theparameters are unchanged from the default options:

Usage:

om -model=<model_fname>[-q=]query [-db=]database [options]

-model=<model_fname> Specifies the model that you want to run. Allmodels supplied by Compugen are located in the directory$CGNROOT/models/.

Valid Command Line Parameters:

-dev=<dev_name> Selects the device to be used by the application.

Valid devices are:

-   -   bic—Bioccelerator (valid for SW, XSW, FRAME_N2P, and FRAME_P2N        models).    -   xlg—BioXLUG (valid for all models except XSW).    -   xlp—BioXIJP (valid for SW, FRAME+_N2P, and FRAME_P2N models).    -   xlh—BioXL/H (valid for SW, FRAME+_N2P, and FRAME_P2N models).    -   soft—Software device (for all models).        -q=<query> Defines the query set. The query can be a sequence        file or a database reference. You can specify a query by its        name or by accession number. The format is detected        automatically. However, you may specify a format using the -qfmt        parameter. If you do not specify a query, the program prompts        for one. If the query set is a database reference, an output        file is produced for each sequence in the query.        -db=<database name> Chooses the database set. The database set        can be a sequence file or a database reference. The database        format is detected automatically. However, you may specify a        format using -dfmt parameter.        -qacc Add this parameter to the command line if you specify        query using accession numbers.        -dacc Add this parameter to the command line if you specify a        database using accession numbers.        -dfmt/-qfmt=<format_type> Chooses the database/query format        type. Possible formats are:    -   fasta—fasta with seq type auto-detected.    -   fastap—fasta protein seq.    -   fastan—fasta nucleic seq.    -   gcg—gcg format, type is auto-detected.    -   gcg9seq—gcg9 format, type is auto-detected.    -   gcg9seqp—gcg9 format protein seq.    -   gcg9seqn—gcg9 format nucleic seq.    -   nbrf—nbrf seq, type is auto-detected.    -   nbrfp—nbrf protein seq.    -   nbrfn—nbrf nucleic seq.    -   embl—embl and swissprot format.    -   genbank—genbank format (nucleic).    -   blast—blast format.    -   nbrf_gcg—nbrf-gcg seq, type is auto-detected.    -   nbrf_gcgp—nbrf-gcg protein seq.    -   nbrf_gcgn—nbrf-gcg nucleic seq.    -   raw—raw ascii sequence, type is auto-detected.    -   rawp—raw ascii protein sequence.    -   rawn—raw ascii nucleic sequence.    -   pir—pir codata format, type is auto-detected.    -   profile—gcg profile (valid only for -qfmt in SW, XSW, FRAME_P2N,        and FRAME+_P2N).        -out=<out_fname> The name of the output file.        -suffix=<name> The output file name suffix.        -gapop=<n> Gap open penalty. This parameter is not valid for        FRAME+. For FrameSearch the default is 12.0. For other searches        the default is 10.0.        -gapext=<n> Gap extend penalty. This parameter is not valid for        FRAME+. For FrameSearch the default is 4.0. For other models:        the default for protein searches is 0.05, and the default for        nucleic searches is 1.0.        -qgapop=<n> The penalty for opening a gap in the query sequence.        The default is 10.0. Valid for XSW.        -qgapext=<n> The penalty for extending a gap in the query        sequence. The default is 0.05. Valid for XSW.        -start=<n> The position in the query sequence to begin the        search.        -end=<n> The position in the query sequence to stop the search.        -qtrans Performs a translated search, relevant for a nucleic        query against a protein database. The nucleic query is        translated to six reading frames and a result is given for each        frame.

Valid for SW and XSW.

-dtrans Performs a translated search, relevant for a protein queryagainst a DNA database. Each database entry is translated to six readingframes and a result is given for each frame.

Valid for SW and XSW.

Note: “-qtrans” and “-dtrans” options are mutually exclusive.

-matrix=<matrix_file> Specifies the comparison matrix to be used in thesearch. The matrix must be in the BLAST format. If the matrix file isnot located in $CGNROOT/tables/matrix, specify the full path as thevalue of the -matrix parameter.

-trans=<transtab_name> Translation table. The default location for thetable is $CGNROOT/tables/trans.

-onestrand Restricts the search to just the top strand of thequery/database nucleic sequence.

-list=<n> The maximum size of the output hit list. The default is 50.

-docalign=<n> The number of documentation lines preceding eachalignment. The default is 10.

-thr_score=<score_name> The score that places limits on the display ofresults. Scores that are smaller than -thr_min value or larger than-thr_max value are not shown. Valid options are: quality.

-   -   zscore.    -   escore.        -thr_max=<n> The score upper threshold. Results that are larger        than -thr_max value are not shown.        -thr_min=<n> The score lower threshold. Results that are lower        than -thr_min value are not shown.        -align=<n> The number of alignments reported in the output file.        -noalign Do not display alignment.        Note: “-align” and “-noalign” parameters are mutually exclusive.        -outfmt=<format_name> Specifies the output format type. The        default format is PFS.        Possible values are:    -   PFS—PFS text format    -   FASTA—FASTA text format    -   BLAST—BLAST text format        -nonorm Do not perform score normalization.        -norm=<norm_name> Specifies the normalization method. Valid        options are:    -   log—logarithm normalization.    -   std—standard normalization.    -   stat—Pearson statistical method.        Note: “-nonorm” and “-norm” parameters cannot be used together.        Note: Parameters -xgapop, -xgapext, -fgapop, -fgapext, -ygapop,        -ygapext, -delop, and -delext apply only to FRAME+.        -xgapop=<n> The penalty for opening a gap when inserting a codon        (triplet). The default is 12.0.        -xgapext=<n> The penalty for extending a gap when inserting a        codon (triplet). The default is 4.0.        -ygapop=<n> The penalty for opening a gap when deleting an amino        acid. The default is 12.0.        -ygapext=<n> The penalty for extending a gap when deleting an        amino acid. The default is 4.0.        -fgapop=<n> The penalty for opening a gap when inserting a DNA        base. The default is 6.0.        -fgapext=<n> The penalty for extending a gap when inserting a        DNA base. The default is 7.0.        -delop=<n> The penalty for opening a gap when deleting a DNA        base. The default is 6.0.        -delext=<n> The penalty for extending a gap when deleting a DNA        base. The default is 7.0.        -silent No screen output is produced.        -host=<host_name> The name of the host on which the server runs.        By default, the application uses the host specified in the file        $CGNROOT/cgnhosts.        -wait Do not go to the background when the device is busy. This        option is not relevant for the Parseq or Soft pseudo device.        -batch Run the job in the background. When this option is        specified, the file “$CGNROOT/defaults/batch.defaults” is used        for choosing the batch command. If this file does not exist, the        command “at now” is used to run the job.        Note: “-batch” and “-wait” parameters are mutually exclusive.        -version Prints the software version number.        -help Displays this help message. To get more specific help        type:    -   “om -model=<model_fname>-help”.

According to some embodiments the homology is a local homology or alocal identity.

Local alignments tools include, but are not limited to the BlastP,BlastN, BlastX or TBLASTN software of the National Center ofBiotechnology Information (NCBI), FASTA, and the Smith-Watermanalgorithm.

A tblastn search allows the comparison between a protein sequence andthe six-frame translations of a nucleotide database. It can be a veryproductive way of finding homologous protein coding regions inunannotated nucleotide sequences such as expressed sequence tags (ESTs)and draft genome records (HTG), located in the BLAST databases est andhtgs, respectively.

Default parameters for blastp include: Max target sequences: 100;Expected threshold: e⁻⁵; Word size: 3; Max matches in a query range: 0;Scoring parameters: Matrix—BLOSUM62; filters and masking: Filter—lowcomplexity regions.

Local alignments tools, which can be used include, but are not limitedto, the tBLASTX algorithm, which compares the six-frame conceptualtranslation products of a nucleotide query sequence (both strands)against a protein sequence database. Default parameters include: Maxtarget sequences: 100; Expected threshold: 10; Word size: 3: Max matchesin a query range: 0; Scoring parameters: Matrix—BLOSUM62; filters andmasking: Filter—low complexity regions.

According to some embodiments of the invention, the exogenouspolynucleotide of the invention encodes a polypeptide having an aminoacid sequence at least about 80%, at least about 81%, at least about82%, at least about 83%, at least about 84%, at least about 85%, atleast about 86%, at least about 87%, at least about 88%, at least about89%, at least about 90%, at least about 91%, at least about 92%, atleast about 93%, at least about 94%, at least about 95%, at least about96%, at least about 97%, at least about 98%, at least about 99%, or moresay 100% identical to the amino acid sequence selected from the groupconsisting of SEQ ID NOs: 220-366, 5629-9399, 9400, 9701-9708, 9753-9795and 9796.

According to some embodiments of the invention, the method of increasingyield, growth rate, biomass, vigor, oil content, seed yield, fiberyield, fiber quality, fertilizer use efficiency (e.g., nitrogen useefficiency) and/or abiotic stress of a plant, is effected by expressingwithin the plant an exogenous polynucleotide comprising a nucleic acidsequence encoding a polypeptide at least at least about 80%, at leastabout 81%, at least about 82%, at least about 83%, at least about 84%,at least about 85%, at least about 86%, at least about 87%, at leastabout 88%, at least about 89%, at least about 90%, at least about 91%,at least about 92%, at least about 93%, at least about 94%, at leastabout 95%, at least about 96%, at least about 97%, at least about 98%,at least about 99%, or more say 100% identical to the amino acidsequence selected from the group consisting of SEQ ID NOs: 220-366,5629-9399, 9400, 9701-9708, 9753-9795 and 9796, thereby increasing theyield, growth rate, biomass, vigor, oil content, seed yield, fiberyield, fiber quality, fertilizer use efficiency (e.g., nitrogen useefficiency) and/or abiotic stress of the plant.

According to some embodiments of the invention, the exogenouspolynucleotide encodes a polypeptide consisting of the amino acidsequence set forth by SEQ ID NO: 220-366, 5629-9399, 9400, 9701-9708,9753-9795 or 9796.

According to an aspect of some embodiments of the invention, the methodof increasing yield, growth rate, biomass, vigor, oil content, seedyield, fiber yield, fiber quality, nitrogen use efficiency, and/orabiotic stress of a plant, is effected by expressing within the plant anexogenous polynucleotide comprising a nucleic acid sequence encoding apolypeptide comprising an amino acid sequence selected from the groupconsisting of SEQ ID NOs:220-366, 5629-9399, 9400, 9701-9708, 9753-9795and 9796, thereby increasing the yield, growth rate, biomass, vigor, oilcontent, seed yield, fiber yield, fiber quality, nitrogen useefficiency, and/or abiotic stress of the plant.

According to an aspect of some embodiments of the invention, there isprovided a method of increasing yield, growth rate, biomass, vigor, oilcontent, seed yield, fiber yield, fiber quality, fertilizer useefficiency (e.g., nitrogen use efficiency) and/or abiotic stress of aplant, comprising expressing within the plant an exogenouspolynucleotide comprising a nucleic acid sequence encoding a polypeptideselected from the group consisting of SEQ ID NOs: 220-366, 5629-9399,9400, 9701-9708, 9753-9795 and 9796, thereby increasing the yield,growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiberquality, fertilizer use efficiency (e.g., nitrogen use efficiency)and/or abiotic stress of the plant.

According to some embodiments of the invention, the exogenouspolynucleotide encodes a polypeptide consisting of the amino acidsequence set forth by SEQ ID NO: 220-366, 5629-9399, 9400, 9701-9708,9753-9795 or 9796.

According to some embodiments of the invention the exogenouspolynucleotide comprises a nucleic acid sequence which is at least about80%, at least about 81%, at least about 82%, at least about 83%, atleast about 84%, at least about 85%, at least about 86%, at least about87%, at least about 88%, at least about 89%, at least about 90%, atleast about 91%, at least about 92%, at least about 93%, at least about93%, at least about 94%, at least about 95%, at least about 96%, atleast about 97%, at least about 98%, at least about 99%, e.g., 100%identical to the nucleic acid sequence selected from the groupconsisting of SEQ ID NOs:1-219, 367-5627, 5628, 9688-9700, 9709-9751 and9752.

According to an aspect of some embodiments of the invention, there isprovided a method of increasing yield, biomass, growth rate, vigor, oilcontent, fiber yield, fiber quality, abiotic stress tolerance, and/ornitrogen use efficiency of a plant, comprising expressing within theplant an exogenous polynucleotide comprising a nucleic acid sequence atleast about 80%, at least about 81%, at least about 82% at least about83%, at least about 84%, at least about 85%, at least about 86%, atleast about 87%, at least about 88%, at least about 89%, at least about90%, at least about 91%, at least about 92%, at least about 93%, atleast about 93%, at least about 94%, at least about 95%, at least about96%, at least about 97%, at least about 98%, at least about 99%, e.g.,100% identical to the nucleic acid sequence selected from the groupconsisting of SEQ ID NOs:1-219, 367-5627, 5628, 9688-9700, 9709-9751 and9752, thereby increasing the yield, biomass, growth rate, vigor, oilcontent, fiber yield, fiber quality, abiotic stress tolerance, and/ornitrogen use efficiency of the plant.

According to some embodiments of the invention the exogenouspolynucleotide is at least about 80%, at least about 81%, at least about82%, at least about 83%, at least about 84%, at least about 85%, atleast about 86%, at least about 87%, at least about 88%, at least about89%, at least about 90%, at least about 91%, at least about 92%, atleast about 93%, at least about 93%, at least about 94%, at least about95%, at least about 96%, at least about 97%, at least about 98%, atleast about 99%, e.g., 100% identical to the polynucleotide selectedfrom the group consisting of SEQ ID NOs: 1-219, 367-5627, 5628,9688-9700, 9709-9751 and 9752.

According to some embodiments of the invention the exogenouspolynucleotide is set forth by SEQ ID NO:1-219, 367-5627, 5628,9688-9700, 9709-9751 or 9752.

As used herein the term “polynucleotide” refers to a single or doublestranded nucleic acid sequence which is isolated and provided in theform of an RNA sequence, a complementary polynucleotide sequence (cDNA),a genomic polynucleotide sequence and/or a composite polynucleotidesequences (e.g., a combination of the above).

The term “isolated” refers to at least partially separated from thenatural environment, e.g., from a plant cell.

As used herein the phrase “complementary polynucleotide sequence” refersto a sequence, which results from reverse transcription of messenger RNAusing a reverse transcriptase or any other RNA dependent DNA polymerase.Such a sequence can be subsequently amplified in vivo or in vitro usinga DNA dependent DNA polymerase.

As used herein the phrase “genomic polynucleotide sequence” refers to asequence derived (isolated) from a chromosome and thus it represents acontiguous portion of a chromosome.

As used herein the phrase “composite polynucleotide sequence” refers toa sequence, which is at least partially complementary and at leastpartially genomic. A composite sequence can include some exonalsequences required to encode the polypeptide of the present invention,as well as some intronic sequences interposing therebetween. Theintronic sequences can be of any source, including of other genes, andtypically will include conserved splicing signal sequences. Suchintronic sequences may further include cis acting expression regulatoryelements.

Nucleic acid sequences encoding the polypeptides of the presentinvention may be optimized for expression. Examples of such sequencemodifications include, but are not limited to, an altered G/C content tomore closely approach that typically found in the plant species ofinterest, and the removal of codons atypically found in the plantspecies commonly referred to as codon optimization.

The phrase “codon optimization” refers to the selection of appropriateDNA nucleotides for use within a structural gene or fragment thereofthat approaches codon usage within the plant of interest. Therefore, anoptimized gene or nucleic acid sequence refers to a gene in which thenucleotide sequence of a native or naturally occurring gene has beenmodified in order to utilize statistically-preferred orstatistically-favored codons within the plant. The nucleotide sequencetypically is examined at the DNA level and the coding region optimizedfor expression in the plant species determined using any suitableprocedure, for example as described in Sardana et al. (1996, Plant CellReports 15:677-681). In this method, the standard deviation of codonusage, a measure of codon usage bias, may be calculated by first findingthe squared proportional deviation of usage of each codon of the nativegene relative to that of highly expressed plant genes, followed by acalculation of the average squared deviation. The formula used is: 1SDCU=n=1 N[(Xn˜Yn)/Yn]2/N, where Xn refers to the frequency of usage ofcodon n in highly expressed plant genes, where Yn to the frequency ofusage of codon n in the gene of interest and N refers to the totalnumber of codons in the gene of interest. A Table of codon usage fromhighly expressed genes of dicotyledonous plants is compiled using thedata of Murray et al. (1989. Nuc Acids Res. 17:477-498).

One method of optimizing the nucleic acid sequence in accordance withthe preferred codon usage for a particular plant cell type is based onthe direct use, without performing any extra statistical calculations,of codon optimization Tables such as those provided on-line at the CodonUsage Database through the NIAS (National Institute of AgrobiologicalSciences) DNA bank in Japan (Hypertext Transfer Protocol://World WideWeb (dot) kazusa (dot) or (dot) jp/codon/). The Codon Usage Databasecontains codon usage tables for a number of different species, with eachcodon usage Table having been statistically determined based on the datapresent in Genbank.

By using the above Tables to determine the most preferred or mostfavored codons for each amino acid in a particular species (for example,rice), a naturally-occurring nucleotide sequence encoding a protein ofinterest can be codon optimized for that particular plant species. Thisis effected by replacing codons that may have a low statisticalincidence in the particular species genome with corresponding codons, inregard to an amino acid, that are statistically more favored. However,one or more less-favored codons may be selected to delete existingrestriction sites, to create new ones at potentially useful junctions(5′ and 3′ ends to add signal peptide or termination cassettes, internalsites that might be used to cut and splice segments together to producea correct full-length sequence), or to eliminate nucleotide sequencesthat may negatively affect mRNA stability or expression.

The naturally-occurring encoding nucleotide sequence may already, inadvance of any modification, contain a number of codons that correspondto a statistically-favored codon in a particular plant species.Therefore, codon optimization of the native nucleotide sequence maycomprise determining which codons, within the native nucleotidesequence, are not statistically-favored with regards to a particularplant, and modifying these codons in accordance with a codon usage tableof the particular plant to produce a codon optimized derivative. Amodified nucleotide sequence may be fully or partially optimized forplant codon usage provided that the protein encoded by the modifiednucleotide sequence is produced at a level higher than the proteinencoded by the corresponding naturally occurring or native gene.Construction of synthetic genes by altering the codon usage is describedin for example PCT Patent Application 93/07278.

According to some embodiments of the invention, the exogenouspolynucleotide is a non-coding RNA.

As used herein the phrase ‘non-coding RNA” refers to an RNA moleculewhich does not encode an amino acid sequence (a polypeptide). Examplesof such non-coding RNA molecules include, but are not limited to, anantisense RNA, a pre-miRNA (precursor of a microRNA), or a precursor ofa Piwi-interacting RNA (piRNA).

Non-limiting examples of non-coding RNA polynucleotides are provided inSEQ ID NOs: 921, 1425, 1938, 1939, 2110, 2208, 2257, 2296, 2297, 2309,2445, 2729, 2844, 2918, 3306, 3310-3312, 3414, 3655-3657, 3834-3835,3841, 3849, 3880-3881, 3892, 3902, 5070 and 5493.

According to some embodiments of the invention the exogenouspolynucleotide comprises a nucleic acid sequence which is at least about80%, at least about 81%, at least about 82%, at least about 83%, atleast about 84%, at least about 85%, at least about 86%, at least about87%, at least about 88%, at least about 89%, at least about 90%, atleast about 91%, at least about 92%, at least about 93%, at least about93%, at least about 94%, at least about 95%, at least about 96%, atleast about 97%, at least about 98%, at least about 99%, e.g., 100%identical to the nucleic acid sequence selected from the groupconsisting of SEQ ID NOs: 1-219, 367-5627, 5628, 9688-9700, 9709-9751and 9752.

According to an aspect of some embodiments of the invention, there isprovided a method of increasing yield, growth rate, biomass, vigor, oilcontent, seed yield, fiber yield, fiber quality, fertilizer useefficiency (e.g., nitrogen use efficiency), and/or abiotic stress of aplant, comprising expressing within the plant an exogenouspolynucleotide comprising a nucleic acid sequence at least about 80%, atleast about 81%, at least about 82%, at least about 83%, at least about84%, at least about 85%, at least about 86%, at least about 87%, atleast about 88%, at least about 89%, at least about 90%, at least about91%, at least about 92%, at least about 93%, at least about 93%, atleast about 94%, at least about 95%, at least about 96%, at least about97%, at least about 98%, at least about 99%, e.g., 100% identical to thenucleic acid sequence selected from the group consisting of SEQ IDNOs:1-219, 367-5627, 5628, 9688-9700, 9709-9751 and 9752, therebyincreasing the yield, growth rate, biomass, vigor, oil content, seedyield, fiber yield, fiber quality, fertilizer use efficiency (e.g.,nitrogen use efficiency), and/or abiotic stress of the plant.

According to some embodiments of the invention the exogenouspolynucleotide is at least about 80%, at least about 81%, at least about82%, at least about 83%, at least about 84%, at least about 85%, atleast about 86%, at least about 87%, at least about 88%, at least about89%, at least about 90%, at least about 91%, at least about 92%, atleast about 93%, at least about 93%, at least about 94%, at least about95%, at least about 96%, at least about 97%, at least about 98%, atleast about 99%, e.g., 100% identical to the polynucleotide selectedfrom the group consisting of SEQ ID NOs: 1-219, 367-5627, 5628,9688-9700, 9709-9751 and 9752.

According to some embodiments of the invention the exogenouspolynucleotide is set forth by SEQ ID NOs: 1-219, 367-5627, 5628,9688-9700, 9709-9751 and 9752.

As used herein the term “polynucleotide” refers to a single or doublestranded nucleic acid sequence which is isolated and provided in theform of an RNA sequence, a complementary polynucleotide sequence (cDNA),a genomic polynucleotide sequence and/or a composite polynucleotidesequences (e.g., a combination of the above).

Thus, the invention encompasses nucleic acid sequences describedhereinabove; fragments thereof, sequences hybridizable therewith,sequences homologous thereto, sequences encoding similar polypeptideswith different codon usage, altered sequences characterized bymutations, such as deletion, insertion or substitution of one or morenucleotides, either naturally occurring or man induced, either randomlyor in a targeted fashion.

The invention provides an isolated polynucleotide comprising a nucleicacid sequence at least about 80%, at least about 81%, at least about82%, at least about 83%, at least about 84%, at least about 85%, atleast about 86%, at least about 87%, at least about 88%, at least about89%, at least about 90%, at least about 91%, at least about 92%, atleast about 93%, at least about 93%, at least about 94%, at least about95%, at least about 96%, at least about 97%, at least about 98%, atleast about 99%, e.g., 100% identical to the polynucleotide selectedfrom the group consisting of SEQ ID NOs: 1-219, 367-5627, 5628,9688-9700, 9709-9751 and 9752.

According to some embodiments of the invention the nucleic acid sequenceis capable of increasing yield, seed yield, growth rate, vigor, biomass,oil content, nitrogen use efficiency, fertilizer use efficiency, fiberyield, fiber quality, abiotic stress tolerance and/or water useefficiency of a plant.

According to some embodiments of the invention the isolatedpolynucleotide comprising the nucleic acid sequence selected from thegroup consisting of SEQ ID NOs: 1-219, 367-5627, 5628, 9688-9700,9709-9751 and 9752.

According to some embodiments of the invention the isolatedpolynucleotide is set forth by SEQ ID NOs: 1-219, 367-5627, 5628,9688-9700, 9709-9751 and 9752.

The invention provides an isolated polynucleotide comprising a nucleicacid sequence encoding a polypeptide which comprises an amino acidsequence at least about 80%, at least about 81%, at least about 82%, atleast about 83%, at least about 84%, at least about 85%, at least about86%, at least about 87%, at least about 88%, at least about 89%, atleast about 90%, at least about 91%, at least about 92%, at least about93%, at least about 93%, at least about 94%, at least about 95%, atleast about 96%, at least about 97%, at least about 98%, at least about99%, or more say 100% homologous to the amino acid sequence selectedfrom the group consisting of SEQ ID NOs: 220-366, 5629-9399, 9400,9701-9708, 9753-9795 and 9796.

According to some embodiments of the invention the amino acid sequenceis capable of increasing yield, growth rate, biomass, vigor, oilcontent, seed yield, fiber yield, fiber quality, fertilizer useefficiency (e.g., nitrogen use efficiency), abiotic stress and/or wateruse efficiency of a plant.

The invention provides an isolated polynucleotide comprising a nucleicacid sequence encoding a polypeptide which comprises the amino acidsequence selected from the group consisting of SEQ ID NOs: 220-366,5629-9399, 9400, 9701-9708, 9753-9795 and 9796.

According to an aspect of some embodiments of the invention, there isprovided a nucleic acid construct comprising the isolated polynucleotideof the invention, and a promoter for directing transcription of thenucleic acid sequence in a host cell. The invention provides an isolatedpolypeptide comprising an amino acid sequence at least about 80%, atleast about 81%, at least about 82%, at least about 83%, at least about84%, at least about 85%, at least about 86%, at least about 87%, atleast about 88%, at least about 89%, at least about 90%, at least about91%, at least about 92%, at least about 93%, at least about 93%, atleast about 94%, at least about 95%, at least about 96%, at least about97%, at least about 98%, at least about 99%, or more say 100% homologousto an amino acid sequence selected from the group consisting of SEQ IDNO: 220-366, 5629-9399, 9400, 9701-9708, 9753-9795 or 9796.

According to some embodiments of the invention, the polypeptidecomprising an amino acid sequence selected from the group consisting ofSEQ ID NOs: 220-366, 5629-9399, 9400, 9701-9708, 9753-9795 and 9796.

According to some embodiments of the invention, the polypeptide is setforth by SEQ ID NOs: 220-366, 5629-9399, 9400, 9701-9708, 9753-9795 and9796.

The invention also encompasses fragments of the above describedpolypeptides and polypeptides having mutations, such as deletions,insertions or substitutions of one or more amino acids, either naturallyoccurring or man induced, either randomly or in a targeted fashion.

The term “‘plant” as used herein encompasses whole plants, ancestors andprogeny of the plants and plant parts, including seeds, shoots, stems,roots (including tubers), and plant cells, tissues and organs. The plantmay be in any form including suspension cultures, embryos, meristematicregions, callus tissue, leaves, gametophytes, sporophytes, pollen, andmicrospores. Plants that are particularly useful in the methods of theinvention include all plants which belong to the superfamilyViridiplantae, in particular monocotyledonous and dicotyledonous plantsincluding a fodder or forage legume, ornamental plant, food crop, tree,or shrub selected from the list comprising Acacia spp., Acer spp.,Actinidia spp., Aesculus spp., Agathis australis, Albizia amara,Alsophila tricolor, Andropogon spp., Arachis spp, Areca catechu, Asteliafragrans, Astragalus cicer, Baikiaea plurijuga, Betula spp., Brassicaspp., Bruguiera gymnorrhiza, Burkea africana, Butea frondosa, Cadabafarinosa, Calliandra spp, Camellia sinensis, Canna indica, Capsicumspp., Cassia spp., Centroema pubescens, Chacoomeles spp., Cinnamomumcassia, Coffea arabica, Colophospermum mopane, Coronillia varia,Cotoneaster serotina, Crataegus spp., Cucumis spp., Cupressus spp.,Cyathea dealbata, Cydonia oblonga, Cryptomeria japonica, Cymbopogonspp., Cynthea dealbata, Cydonia oblonga, Dalbergia monetaria, Davalliadivaricata, Desmodium spp., Dicksonia squarosa, Dibeteropogonamplectens, Dioclea spp, Dolichos spp., Dorycnium rectum, Echinochloapyramidalis, Ehraffia spp., Eleusine coracana, Eragrestis spp.,Erythrina spp., Eucalypfus spp., Euclea schimperi, Eulalia vi/losa,Pagopyrum spp., Feijoa sellowlana, Fragaria spp., Flemingia spp,Freycinetia banksli, Geranium thunbergii, GinAgo biloba, Glycinejavanica, Gliricidia spp, Gossypium hirsutum, Grevillea spp., Guibourtiacoleosperma, Hedysarum spp., Hemaffhia altissima, Heteropogon contoffus,Hordeum vulgare, Hyparrhenia rufa, Hypericum erectum, Hypeffheliadissolute, Indigo incamata, Iris spp., Leptarrhena pyrolifolia,Lespediza spp., Lettuca spp., Leucaena leucocephala, Loudetia simplex,Lotonus bainesli, Lotus spp., Macrotyloma axillare, Malus spp., Manihotesculenta, Medicago saliva, Metasequoia glyptostroboides, Musasapientum, Nicotianum spp., Onobrychis spp., Ornithopus spp., Oryzaspp., Peltophorum africanum, Pennisetum spp., Persea gratissima, Petuniaspp., Phaseolus spp., Phoenix canariensis, Phormium cookianum, Photiniaspp., Picea glauca, Pinus spp., Pisum sativam, Podocarpus totara,Pogonarthria fleckii, Pogonaffhria squarrosa, Populus spp., Prosopiscineraria, Pseudotsuga menziesii, Pterolobium stellatum, Pyrus communis,Quercus spp., Rhaphiolepsis umbellata, Rhopalostylis sapida, Rhusnatalensis, Ribes grossularia, Ribes spp., Robinia pseudoacacia, Rosaspp., Rubus spp., Salix spp., Schyzachyrium sanguineum, Sciadopitysvefficillata, Sequoia sempervirens, Sequoiadendron giganteum, Sorghumbicolor, Spinacia spp., Sporobolus fimbriatus, Stiburus alopecuroides,Stylosanthos humilis, Tadehagi spp, Taxodium distichum, Themedatriandra, Trifolium spp., Triticum spp., Tsuga heterophylla, Vacciniumspp., Vicia spp., Vitis vinifera, Watsonia pyramidata, Zantedeschiaaethiopica, Zea mays, amaranth, artichoke, asparagus, broccoli. Brusselssprouts, cabbage, canola, carrot, cauliflower, celery, collard greens,flax, kale, lentil, oilseed rape, okra, onion, potato, rice, soybean,straw, sugar beet, sugar cane, sunflower, tomato, squash tea, maize,wheat, barley, rye, oat, peanut, pea, lentil and alfalfa, cotton,rapeseed, canola, pepper, sunflower, tobacco, eggplant, eucalyptus, atree, an ornamental plant, a perennial grass and a forage crop.Alternatively algae and other non-Viridiplantae can be used for themethods of the present invention.

According to some embodiments of the invention, the plant used by themethod of the invention is a crop plant such as rice, maize, wheat,barley, peanut, potato, sesame, olive tree, palm oil, banana, soybean,sunflower, canola, sugarcane, alfalfa, millet, leguminosae (bean, pea),flax, lupinus, rapeseed, tobacco, poplar and cotton.

According to some embodiments of the invention, the plant used by themethod of the invention is wheat.

Non-limiting examples of wheat species which can be used according tosome embodiments of the invention include Faller, Bobwhite, Mc Neal,Anshlag, KWS Aurum, KWS Scirocco and Azhurnaya.

According to some embodiments of the invention the plant is adicotyledonous plant.

According to some embodiments of the invention the plant is amonocotyledonous plant.

According to some embodiments of the invention, there is provided aplant cell exogenously expressing the polynucleotide of some embodimentsof the invention, the nucleic acid construct of some embodiments of theinvention and/or the polypeptide of some embodiments of the invention.

According to some embodiments of the invention, expressing the exogenouspolynucleotide of the invention within the plant is effected bytransforming one or more cells of the plant with the exogenouspolynucleotide, followed by generating a mature plant from thetransformed cells and cultivating the mature plant under conditionssuitable for expressing the exogenous polynucleotide within the matureplant.

According to some embodiments of the invention, the transformation iseffected by introducing to the plant cell a nucleic acid construct whichincludes the exogenous polynucleotide of some embodiments of theinvention and at least one promoter for directing transcription of theexogenous polynucleotide in a host cell (a plant cell). Further detailsof suitable transformation approaches are provided hereinbelow.

As mentioned, the nucleic acid construct according to some embodimentsof the invention comprises a promoter sequence and the isolatedpolynucleotide of the invention.

According to some embodiments of the invention, the isolatedpolynucleotide is operably linked to the promoter sequence.

A coding nucleic acid sequence is “operably linked” to a regulatorysequence (e.g., promoter) if the regulatory sequence is capable ofexerting a regulatory effect on the coding sequence linked thereto.

As used herein, the term “promoter” refers to a region of DNA which liesupstream of the transcriptional initiation site of a gene to which RNApolymerase binds to initiate transcription of RNA. The promoter controlswhere (e.g., which portion of a plant) and/or when (e.g., at which stageor condition in the lifetime of an organism) the gene is expressed.

According to some embodiments of the invention, the promoter isheterologous to the isolated polynucleotide and/or to the host cell.

As used herein the phrase “heterologous promoter” refers to a promoterfrom a different species or from the same species but from a differentgene locus as of the isolated polynucleotide sequence.

Any suitable promoter sequence can be used by the nucleic acid constructof the present invention. Preferably the promoter is a constitutivepromoter, a tissue-specific, or an abiotic stress-inducible promoter.

According to some embodiments of the invention, the promoter is a plantpromoter, which is suitable for expression of the exogenouspolynucleotide in a plant cell.

According to some embodiments of the invention, the promoter is a wheatpromoter (i.e., a promoter which is suitable for expression in wheatplants).

Suitable promoters for expression in wheat include, but are not limitedto, Wheat SPA promoter (SEQ ID NO: 9811; Albani et al, Plant Cell, 9:171-184, 1997, which is fully incorporated herein by reference), wheatLMW [SEQ ID NO: 9806 (longer LMW promoter), and SEQ ID NO: 9807 (LMWpromoter)] and HMW glutenin-1 [SEQ ID NO: 9804 (Wheat HMW glutenin-1longer promoter); and SEQ ID NO: 9805 (Wheat HMW glutenin-1 Promoter);Thomas and Flavell, The Plant Cell 2:1171-1180; Furtado et al., 2009Plant Biotechnology Journal 7:240-253, each of which is fullyincorporated herein by reference], wheat alpha, beta and gamma gliadins[e.g., SEQ ID NO: 9812 (wheat alpha gliadin, B genome, promoter); SEQ IDNO: 9813 (wheat gamma gliadin promoter): EMBO 3:1409-15, 1984, which isfully incorporated herein by reference], wheat TdPR60 [SEQ ID NO:9809(wheat TdPR60 longer promoter) or SEQ ID NO:9810 (wheat TdPR60promoter); Kovalchuk et al., Plant Mol Biol 71:81-98, 2009, which isfully incorporated herein by reference], maize Ub1 Promoter [cultivarNongda 105 (SEQ ID NO:9406); GenBank: DQ141598.1; Taylor et al., PlantCell Rep 1993 12: 491-495, which is fully incorporated herein byreference; and cultivar B73 (SEQ ID NO:9409); Christensen, A H, et al.Plant Mol. Biol. 18 (4), 675-689 (1992), which is fully incorporatedherein by reference]; rice actin 1 (SEQ ID NO:9407; Mc Elroy et al.1990, The Plant Cell, Vol. 2, 163-171, which is fully incorporatedherein by reference), rice GOS2 [SEQ ID NO: 9408 (rice GOS2 longerpromoter) and SEQ ID NO: 9797 (rice GOS2 Promoter); De Pater et al.Plant J. 1992; 2: 837-44, which is fully incorporated herein byreference], arabidopsis Phol [SEQ ID NO: 9418 (arabidopsis PholPromoter): Hamburger et al., Plant Cell. 2002; 14: 889-902, which isfully incorporated herein by reference], ExpansinB promoters, e.g., riceExpB5 [SEQ ID NO:9799 (rice ExpB5 longer promoter) and SEQ ID NO: 9800(rice ExpB5 promoter)] and Barley ExpB1 [SEQ ID NO: 9801 (barley ExpB1Promoter), Won et al. Mol Cells. 2010: 30:369-76, which is fullyincorporated herein by reference], barley SS2 (sucrose synthase 2) [(SEQID NO: 9808), Guerin and Carbonero, Plant Physiology May 1997 vol. 114no. 1 55-62, which is fully incorporated herein by reference], and ricePG5a [SEQ ID NO:9803, U.S. Pat. No. 7,700,835, Nakase et al., Plant MolBiol. 32:621-30, 1996, each of which is fully incorporated herein byreference].

Suitable constitutive promoters include, for example. CaMV 35S promoter[SEQ ID NO: 9401 (CaMV 35S (QFNC) Promoter); SEQ ID NO: 9402 (PJJ 35Sfrom Brachypodium); SEQ ID NO: 9403 (CaMV 35S (OLD) Promoter) (Odell etal., Nature 313:810-812, 1985)], Arabidopsis At6669 promoter (SEQ ID NO:9404 (Arabidopsis At6669 (OLD) Promoter); see PCT Publication No.WO04081173A2 or the new At6669 promoter (SEQ ID NO: 9405 (ArabidopsisAt6669 (NEW) Promoter)); maize Ub1 Promoter [cultivar Nongda 105 (SEQ IDNO:9406); GenBank: DQ141598.1: Taylor et al., Plant Cell Rep 1993 12:491-495, which is fully incorporated herein by reference; and cultivarB73 (SEQ ID NO:9409); Christensen, A H, et al. Plant Mol. Biol. 18 (4),675-689 (1992), which is fully incorporated herein by reference]; riceactin 1 (SEQ ID NO: 9407. McElroy et al., Plant Cell 2:163-171, 1990);pEMU (Last et al., Theor. Appl. Genet. 81:581-588, 1991); CaMV 19S(Nilsson et al., Physiol. Plant 100:456-462, 1997); rice GOS2 [SEQ IDNO: 9408 (rice GOS2 longer Promoter) and SEQ ID NO: 9797 (rice GOS2Promoter), de Pater et al, Plant J November; 2(6):837-44, 1992]; RBCSpromoter (SEQ ID NO:9410); Rice cyclophilin (Bucholz et al, Plant MolBiol. 25(5):837-43, 1994); Maize H3 histone (Lepetit et al. Mol. Gen.Genet. 231: 276-285, 1992); Actin 2 (An et al, Plant J. 10(1); 107-121,1996) and Synthetic Super MAS (Ni et al., The Plant Journal 7: 661-76,1995). Other constitutive promoters include those in U.S. Pat. Nos.5,659,026, 5,608,149; 5,608,144; 5,604,121; 5,569,597; 5,466,785;5,399,680; 5,268,463; and 5,608,142.

Suitable tissue-specific promoters include, but not limited to,leaf-specific promoters [e.g., AT5G06690 (Thioredoxin) (high expression,SEQ ID NO: 9411), AT5G61520 (AtSTP3) (low expression. SEQ ID NO: 9412)described in Buttner et al 2000 Plant, Cell and Environment 23, 175-184,or the promoters described in Yamamoto et al., Plant J. 12:255-265,1997; Kwon et al., Plant Physiol. 105:357-67, 1994; Yamamoto et al.,Plant Cell Physiol. 35:773-778, 1994; Gotor et al., Plant J. 3:509-18,1993; Orozco et al., Plant Mol. Biol. 23:1129-1138, 1993; and Matsuokaet al., Proc. Natl. Acad. Sci. USA 90:9586-9590, 1993; as well asArabidopsis STP3 (AT5G61520) promoter (Buttner et al., Plant, Cell andEnvironment 23:175-184, 2000)], seed-preferred promoters [e.g., Napin(originated from Brassica napus which is characterized by a seedspecific promoter activity; Stuitje A. R. et. al. Plant BiotechnologyJournal 1 (4): 301-309; SEQ ID NO: 9413 (Brassica napus NAPIN Promoter)from seed specific genes (Simon, et al., Plant Mol. Biol. 5, 191, 1985;Scofield, et al., J. Biol. Chem. 262: 12202, 1987; Baszczynski, et al.,Plant Mol. Biol. 14: 633, 1990), rice PG5a (SEQ ID NO: 9803: U.S. Pat.No. 7,700,835), early seed development Arabidopsis BAN (AT1G61720) (SEQID NO: 9414, US 2009/0031450 A1), late seed development Arabidopsis ABI3(AT3G24650) (SEQ ID NOs: 9415 (Arabidopsis ABI3 (AT3G24650) longerPromoter) or 9802 (Arabidopsis ABI3 (AT3G24650) Promoter)) (Ng et al.,Plant Molecular Biology 54: 25-38, 2004), Brazil Nut albumin (Pearson'et al., Plant Mol. Biol. 18: 235-245, 1992), legumin (Ellis. et al.Plant Mol. Biol. 10: 203-214, 1988). Glutelin (rice) (Takaiwa, et al.,Mol. Gen. Genet. 208: 15-22, 1986; Takaiwa, et al., FEBS Letts. 221:43-47, 1987), Zein (Matzke et al Plant Mol Biol, 143). 323-32 1990),napA (Stalberg, et al, Planta 199: 515-519, 1996), Wheat SPA (SEQ IDNO:9811; Albani et al. Plant Cell, 9: 171-184, 1997), sunflower oleosin(Cummins. et al., Plant Mol. Biol. 19: 873-876, 1992)], endospermspecific promoters [e.g., wheat LMW (SEQ ID NO: 9806 (Wheat LMW LongerPromoter), and SEQ ID NO: 9807 (Wheat LMW Promoter) and HMW glutenin-1[(SEQ ID NO: 9804 (Wheat HMW glutenin-1 longer Promoter)); and SEQ IDNO: 9805 (Wheat HMW glutenin-1 Promoter), Thomas and Flavell, The PlantCell 2:1171-1180, 1990; Mol Gen Genet 216:81-90, 1989; NAR 17:461-2),wheat alpha, beta and gamma gliadins (SEQ ID NO: 9812 (wheat alphagliadin (B genome) promoter): SEQ ID NO: 9813 (wheat gamma gliadinpromoter); EMBO 3:1409-15, 1984). Barley ltrl promoter, barley B1, C. Dhordein (Theor Appl Gen 98:1253-62, 1999: Plant J 4:343-55, 1993; MolGen Genet 250:750-60, 1996), Barley DOF (Mena et al., The Plant Journal,116(1): 53-62, 1998), Biz2 (EP99106056.7), Barley SS2 (SEQ ID NO: 9808(Barley SS2 Promoter): Guerin and Carbonero Plant Physiology 114: 155-62, 1997), wheat TdPR60 [SEQ ID NO:9809 (wheat TdPR60 longerpromoter) or SEQ ID NO:9810 (wheat TdPR60 promoter): Kovalchuk et al.,Plant Mol Biol 71:81-98, 2009, which is fully incorporated herein byreference], barley D-hordein (D-Hor) and B-hordein (B-Hor) (AgneloFurtado, Robert J. Henry and Alessandro Pellegrineschi (2009)],Synthetic promoter (Vicente-Carbajosa et al., Plant J. 13: 629-640,1998), rice prolamin NRP33, rice -globulin Glb-1 (Wu et al. Plant CellPhysiology 39(8) 885-889, 1998), rice alpha-globulin REB/OHP-1 (Nakaseet al. Plant Mol. Biol. 33: 513-S22, 1997), rice ADP-glucose PP (TransRes 6:157-68, 1997), maize ESR gene family (Plant J 12:235-46, 1997),sorgum gamma-kafirin (PMB 32:1029-35, 1996)], embryo specific promoters[e.g., rice OSH1 (Sato et al. Proc. Natl. Acad. Sci. USA. 93:8117-8122), KNOX (Postma-Haarsma ef al. Plant Mol. Biol. 39:257-71,1999), rice oleosin (Wu et at, J. Biochem., 123:386, 1998)], andflower-specific promoters [e.g., AtPRP4, chalene synthase (chsA) (Vander Meer. et al., Plant Mol. Biol. 15, 95-109, 1990), LAT52 (Twell et alMol. Gen Genet. 217:240-245; 1989). Arabidopsis apetala-3 (Tilly et al.,Development. 125:1647-57, 1998), Arabidopsis APETALA 1 (AT1G69120, API)(SEQ ID NO: 9416 (Arabidopsis (AT1G69120) APETALA 1)) (Hempel et al.,Development 124:3845-3853, 1997)], and root promoters [e.g., the ROOTPpromoter [SEQ ID NO: 9417]; rice ExpB5 (SEQ ID NO:9800 (rice ExpB5Promoter); or SEQ ID NO: 9799 (rice ExpB5 longer Promoter)) and barleyExpB1 promoters (SEQ ID NO:9801) (Won et al. Mol. Cells 30: 369-376,2010); arabidopsis ATTPS-CIN (AT3G25820) promoter (SEQ ID NO: 9798; Chenet al., Plant Phys 135:1956-66, 2004); arabidopsis Phol promoter (SEQ IDNO: 9418. Hamburger et al., Plant Cell. 14: 889-902, 2002), which isalso slightly induced by stress].

Suitable abiotic stress-inducible promoters include, but not limited to,salt-inducible promoters such as RD29A (Yamaguchi-Shinozalei et al.,Mol. Gen. Genet. 236:331-340, 1993); drought-inducible promoters such asmaize rab17 gene promoter (Pla et. al., Plant Mol. Biol. 21:259-266,1993), maize rab28 gene promoter (Busk et. al., Plant J. 11:1285-1295,1997) and maize Ivr2 gene promoter (Pelleschi et. al., Plant Mol. Biol.39:373-380, 1999); heat-inducible promoters such as heat tomatohsp80-promoter from tomato (U.S. Pat. No. 5,187,267).

The nucleic acid construct of some embodiments of the invention canfurther include an appropriate selectable marker and/or an origin ofreplication. According to some embodiments of the invention, the nucleicacid construct utilized is a shuttle vector, which can propagate both inE. coli (wherein the construct comprises an appropriate selectablemarker and origin of replication) and be compatible with propagation incells. The construct according to the present invention can be, forexample, a plasmid, a bacmid, a phagemid, a cosmid, a phage, a virus oran artificial chromosome.

The nucleic acid construct of some embodiments of the invention can beutilized to stably or transiently transform plant cells. In stabletransformation, the exogenous polynucleotide is integrated into theplant genome and as such it represents a stable and inherited trait. Intransient transformation, the exogenous polynucleotide is expressed bythe cell transformed but it is not integrated into the genome and assuch it represents a transient trait.

There are various methods of introducing foreign genes into bothmonocotyledonous and dicotyledonous plants (Potrykus. I., Annu. Rev.Plant. Physiol., Plant. Mol. Biol. (1991) 42:205-225; Shimamoto et al.,Nature (1989) 338:274-276).

The principle methods of causing stable integration of exogenous DNAinto plant genomic DNA include two main approaches:

(i) Agrobacterium-mediated gene transfer: Klee et al. (1987) Annu. Rev.Plant Physiol. 38:467-486; Klee and Rogers in Cell Culture and SomaticCell Genetics of Plants. Vol. 6, Molecular Biology of Plant NuclearGenes, eds. Schell. J., and Vasil, L. K., Academic Publishers, SanDiego. Calif. (1989) p. 2-25; Gatenby, in Plant Biotechnology, eds.Kung. S, and Arntzen, C. J., Butterworth Publishers, Boston, Mass.(1989) p. 93-112.

(ii) Direct DNA uptake: Paszkowski et al., in Cell Culture and SomaticCell Genetics of Plants. Vol. 6, Molecular Biology of Plant NuclearGenes eds. Schell. J., and Vasil, L. K., Academic Publishers, San Diego,Calif. (1989) p. 52-68; including methods for direct uptake of DNA intoprotoplasts. Toriyama. K. et al. (1988) Bio/Technology 6:1072-1074. DNAuptake induced by brief electric shock of plant cells: Zhang et al.Plant Cell Rep. (1988) 7:379-384. Fromm et al. Nature (1986)319:791-793. DNA injection into plant cells or tissues by particlebombardment, Klein et al. Bio/Technology (1988) 6:559-563; McCabe et al.Bio/Technology (1988) 6:923-926; Sanford. Physiol. Plant. (1990)79:206-209; by the use of micropipette systems: Neuhaus et al., Theor.Appl. Genet. (0.1987) 75:30-36; Neuhaus and Spangenberg, Physiol. Plant.(1990) 79:213-217; glass fibers or silicon carbide whiskertransformation of cell cultures, embryos or callus tissue, U.S. Pat. No.5,464,765 or by the direct incubation of DNA with germinating pollen.DeWet et al. in Experimental Manipulation of Ovule Tissue, eds. Chapman,G. P, and Mantell, S. H, and Daniels, W. Longman, London. (1985) p.197-209; and Ohta, Proc. Natl. Acad. Sci. USA (1986) 83:715-719.

The Agrobacterium system includes the use of plasmid vectors thatcontain defined DNA segments that integrate into the plant genomic DNA.Methods of inoculation of the plant tissue vary depending upon the plantspecies and the Agrobacterium delivery system. A widely used approach isthe leaf disc procedure which can be performed with any tissue explantthat provides a good source for initiation of whole plantdifferentiation. See, e.g., Horsch et al. in Plant Molecular BiologyManual A5, Kluwer Academic Publishers. Dordrecht (1988) p. 1-9. Asupplementary approach employs the Agrobacterium delivery system incombination with vacuum infiltration. The Agrobacterium system isespecially viable in the creation of transgenic dicotyledonous plants.

There are various methods of direct DNA transfer into plant cells. Inelectroporation, the protoplasts are briefly exposed to a strongelectric field. In microinjection, the DNA is mechanically injecteddirectly into the cells using very small micropipettes. In microparticlebombardment, the DNA is adsorbed on microprojectiles such as magnesiumsulfate crystals or tungsten particles, and the microprojectiles arephysically accelerated into cells or plant tissues.

Following stable transformation plant propagation is exercised. The mostcommon method of plant propagation is by seed. Regeneration by seedpropagation, however, has the deficiency that due to heterozygositythere is a lack of uniformity in the crop, since seeds are produced byplants according to the genetic variances governed by Mendelian rules.Basically, each seed is genetically different and each will grow withits own specific traits. Therefore, it is preferred that the transformedplant be produced such that the regenerated plant has the identicaltraits and characteristics of the parent transgenic plant. Therefore, itis preferred that the transformed plant be regenerated bymicropropagation which provides a rapid, consistent reproduction of thetransformed plants.

Micropropagation is a process of growing new generation plants from asingle piece of tissue that has been excised from a selected parentplant or cultivar. This process permits the mass reproduction of plantshaving the preferred tissue expressing the fusion protein. The newgeneration plants which are produced are genetically identical to, andhave all of the characteristics of, the original plant. Micropropagationallows mass production of quality plant material in a short period oftime and offers a rapid multiplication of selected cultivars in thepreservation of the characteristics of the original transgenic ortransformed plant. The advantages of cloning plants are the speed ofplant multiplication and the quality and uniformity of plants produced.

Micropropagation is a multi-stage procedure that requires alteration ofculture medium or growth conditions between stages. Thus, themicropropagation process involves four basic stages: Stage one, initialtissue culturing; stage two, tissue culture multiplication; stage three,differentiation and plant formation; and stage four, greenhouseculturing and hardening. During stage one, initial tissue culturing, thetissue culture is established and certified contaminant-free. Duringstage two, the initial tissue culture is multiplied until a sufficientnumber of tissue samples are produced to meet production goals. Duringstage three, the tissue samples grown in stage two are divided and growninto individual plantlets. At stage four, the transformed plantlets aretransferred to a greenhouse for hardening where the plants' tolerance tolight is gradually increased so that it can be grown in the naturalenvironment.

According to some embodiments of the invention, the transgenic plantsare generated by transient transformation of leaf cells, meristematiccells or the whole plant.

Transient transformation can be effected by any of the direct DNAtransfer methods described above or by viral infection using modifiedplant viruses.

Viruses that have been shown to be useful for the transformation ofplant hosts include CaMV, Tobacco mosaic virus (TMV), brome mosaic virus(BMV) and Bean Common Mosaic Virus (BV or BCMV). Transformation ofplants using plant viruses is described in U.S. Pat. No. 4,855,237 (beangolden mosaic virus; BGV). EP-A 67,553 (TMV), Japanese PublishedApplication No. 63-14693 (TMV), EPA 194.809 (BV), EPA 278,667 (BV); andGluzman, Y. et al., Communications in Molecular Biology: Viral Vectors.Cold Spring Harbor Laboratory. New York, pp. 172-189 (1988). Pseudovirusparticles for use in expressing foreign DNA in many hosts, includingplants are described in WO 87/06261.

According to some embodiments of the invention, the virus used fortransient transformations is avirulent and thus is incapable of causingsevere symptoms such as reduced growth rate, mosaic, ring spots, leafroll, yellowing, streaking, pox formation, tumor formation and pitting.A suitable avirulent virus may be a naturally occurring avirulent virusor an artificially attenuated virus. Virus attenuation may be effectedby using methods well known in the art including, but not limited to,sub-lethal heating, chemical treatment or by directed mutagenesistechniques such as described, for example, by Kurihara and Watanabe(Molecular Plant Pathology 4:259-269, 2003). Gal-on et al. (1992),Atreya et al. (1992) and Huet et al. (1994).

Suitable virus strains can be obtained from available sources such as,for example, the American Type culture Collection (ATCC) or by isolationfrom infected plants. Isolation of viruses from infected plant tissuescan be effected by techniques well known in the art such as described,for example by Foster and Tatlor, Eds. “Plant Virology Protocols: FromVirus Isolation to Transgenic Resistance (Methods in Molecular Biology(Humana Pr). Vol 81)”. Humana Press, 1998. Briefly, tissues of aninfected plant believed to contain a high concentration of a suitablevirus, preferably young leaves and flower petals, are ground in a buffersolution (e.g., phosphate buffer solution) to produce a virus infectedsap which can be used in subsequent inoculations.

Construction of plant RNA viruses for the introduction and expression ofnon-viral exogenous polynucleotide sequences in plants is demonstratedby the above references as well as by Dawson, W. O. et al., Virology(1989) 172:285-292; Takamatsu et al. EMBO J. (1987) 6:307-311; French etal. Science (1986) 231:1294-1297; Takamatsu et al. FEBS Letters (1990)269:73-76; and U.S. Pat. No. 5,316,931.

When the virus is a DNA virus, suitable modifications can be made to thevirus itself. Alternatively, the virus can first be cloned into abacterial plasmid for case of constructing the desired viral vector withthe foreign DNA. The virus can then be excised from the plasmid. If thevirus is a DNA virus, a bacterial origin of replication can be attachedto the viral DNA, which is then replicated by the bacteria.Transcription and translation of this DNA will produce the coat proteinwhich encapsidates the viral DNA. If the virus is an RNA virus, thevirus is generally cloned as a cDNA and inserted into a plasmid. Theplasmid is then used to make all of the constructions. The RNA virus isthen produced by transcribing the viral sequence of the plasmid andtranslation of the viral genes to produce the coat protein(s) whichencapsidate the viral RNA.

In one embodiment, a plant viral polynucleotide is provided in which thenative coat protein coding sequence has been deleted from a viralpolynucleotide, a non-native plant viral coat protein coding sequenceand a non-native promoter, preferably the subgenomic promoter of thenon-native coat protein coding sequence, capable of expression in theplant host, packaging of the recombinant plant viral polynucleotide, andensuring a systemic infection of the host by the recombinant plant viralpolynucleotide, has been inserted. Alternatively, the coat protein genemay be inactivated by insertion of the non-native polynucleotidesequence within it, such that a protein is produced. The recombinantplant viral polynucleotide may contain one or more additional non-nativesubgenomic promoters. Each non-native subgenomic promoter is capable oftranscribing or expressing adjacent genes or polynucleotide sequences inthe plant host and incapable of recombination with each other and withnative subgenomic promoters. Non-native (foreign) polynucleotidesequences may be inserted adjacent the native plant viral subgenomicpromoter or the native and a non-native plant viral subgenomic promotersif more than one polynucleotide sequence is included. The non-nativepolynucleotide sequences are transcribed or expressed in the host plantunder control of the subgenomic promoter to produce the desiredproducts.

In a second embodiment, a recombinant plant viral polynucleotide isprovided as in the first embodiment except that the native coat proteincoding sequence is placed adjacent one of the non-native coat proteinsubgenomic promoters instead of a non-native coat protein codingsequence.

In a third embodiment, a recombinant plant viral polynucleotide isprovided in which the native coat protein gene is adjacent itssubgenomic promoter and one or more non-native subgenomic promoters havebeen inserted into the viral polynucleotide. The inserted non-nativesubgenomic promoters are capable of transcribing or expressing adjacentgenes in a plant host and are incapable of recombination with each otherand with native subgenomic promoters. Non-native polynucleotidesequences may be inserted adjacent the non-native subgenomic plant viralpromoters such that the sequences are transcribed or expressed in thehost plant under control of the subgenomic promoters to produce thedesired product.

In a fourth embodiment, a recombinant plant viral polynucleotide isprovided as in the third embodiment except that the native coat proteincoding sequence is replaced by a non-native coat protein codingsequence.

The viral vectors are encapsidated by the coat proteins encoded by therecombinant plant viral polynucleotide to produce a recombinant plantvirus. The recombinant plant viral polynucleotide or recombinant plantvirus is used to infect appropriate host plants. The recombinant plantviral polynucleotide is capable of replication in the host, systemicspread in the host, and transcription or expression of foreign gene(s)(exogenous polynucleotide) in the host to produce the desired protein.

Techniques for inoculation of viruses to plants may be found in Fosterand Taylor, eds. “Plant Virology Protocols: From Virus Isolation toTransgenic Resistance (Methods in Molecular Biology (Humana Pr), Vol81)”, Humana Press, 1998; Maramorosh and Koprowski, eds. “Methods inVirology” 7 vols, Academic Press, New York 1967-1984; Hill, S. A.“Methods in Plant Virology”, Blackwell, Oxford, 1984; Walkey, D. G. A.“Applied Plant Virology”, Wiley, New York, 1985; and Kado and Agrawa,eds. “Principles and Techniques in Plant Virology”, VanNostrand-Reinhold, New York.

In addition to the above, the polynucleotide of the present inventioncan also be introduced into a chloroplast genome thereby enablingchloroplast expression.

A technique for introducing exogenous polynucleotide sequences to thegenome of the chloroplasts is known. This technique involves thefollowing procedures. First, plant cells are chemically treated so as toreduce the number of chloroplasts per cell to about one. Then, theexogenous polynucleotide is introduced via particle bombardment into thecells with the aim of introducing at least one exogenous polynucleotidemolecule into the chloroplasts. The exogenous polynucleotides selectedsuch that it is integratable into the chloroplast's genome viahomologous recombination which is readily effected by enzymes inherentto the chloroplast. To this end, the exogenous polynucleotide includes,in addition to a gene of interest, at least one polynucleotide stretchwhich is derived from the chloroplast's genome. In addition, theexogenous polynucleotide includes a selectable marker, which serves bysequential selection procedures to ascertain that all or substantiallyall of the copies of the chloroplast genomes following such selectionwill include the exogenous polynucleotide. Further details relating tothis technique are found in U.S. Pat. Nos. 4,945,050; and 5,693,507which are incorporated herein by reference. A polypeptide can thus beproduced by the protein expression system of the chloroplast and becomeintegrated into the chloroplast's inner membrane.

Since processes which increase yield, seed yield, fiber yield, fiberquality, fiber length, growth rate, biomass, vigor, nitrogen useefficiency, fertilizer use efficiency, oil content, and/or abioticstress tolerance of a plant can involve multiple genes acting additivelyor in synergy (see, for example, in Quesda et al., Plant Physiol.130:951-063, 2002), the present invention also envisages expressing aplurality of exogenous polynucleotides in a single host plant to therebyachieve superior effect on oil content, yield, growth rate, biomass,vigor and/or abiotic stress tolerance.

Expressing a plurality of exogenous polynucleotides in a single hostplant can be effected by co-introducing multiple nucleic acidconstructs, each including a different exogenous polynucleotide, into asingle plant cell. The transformed cell can then be regenerated into amature plant using the methods described hereinabove.

Alternatively, expressing a plurality of exogenous polynucleotides in asingle host plant can be effected by co-introducing into a singleplant-cell a single nucleic-acid construct including a plurality ofdifferent exogenous polynucleotides. Such a construct can be designedwith a single promoter sequence which can transcribe a polycistronicmessenger RNA including all the different exogenous polynucleotidesequences. To enable co-translation of the different polypeptidesencoded by the polycistronic messenger RNA, the polynucleotide sequencescan be inter-linked via an internal ribosome entry site (IRES) sequencewhich facilitates translation of polynucleotide sequences positioneddownstream of the IRES sequence. In this case, a transcribedpolycistronic RNA molecule encoding the different polypeptides describedabove will be translated from both the capped 5′ end and the twointernal IRES sequences of the polycistronic RNA molecule to therebyproduce in the cell all different polypeptides. Alternatively, theconstruct can include several promoter sequences each linked to adifferent exogenous polynucleotide sequence.

The plant cell transformed with the construct including a plurality ofdifferent exogenous polynucleotides, can be regenerated into a matureplant, using the methods described hereinabove.

Alternatively, expressing a plurality of exogenous polynucleotides in asingle host plant can be effected by introducing different nucleic acidconstructs, including different exogenous polynucleotides, into aplurality of plants. The regenerated transformed plants can then becross-bred and resultant progeny selected for superior abiotic stresstolerance, water use efficiency, fertilizer use efficiency, growth,biomass, yield and/or vigor traits, using conventional plant breedingtechniques.

According to some embodiments of the invention, the method furthercomprising growing the plant expressing the exogenous polynucleotideunder the abiotic stress.

Non-limiting examples of abiotic stress conditions include, salinity,osmotic stress, drought, water deprivation, excess of water (e.g.,flood, waterlogging), etiolation, low temperature, high temperature,heavy metal toxicity, anaerobiosis, nutrient deficiency, nutrientexcess, atmospheric pollution and UV irradiation.

According to some embodiments of the invention, the method furthercomprising growing the plant expressing the exogenous polynucleotideunder fertilizer limiting conditions (e.g., nitrogen-limitingconditions). Non-limiting examples include growing the plant on soilswith low nitrogen content (40-50% Nitrogen of the content present undernormal or optimal conditions), or even under sever nitrogen deficiency(0-10% Nitrogen of the content present under normal or optimalconditions).

Thus, the invention encompasses plants exogenously expressing thepolynucleotide(s), the nucleic acid constructs and/or polypeptide(s) ofthe invention.

Once expressed within the plant cell or the entire plant, the level ofthe polypeptide encoded by the exogenous polynucleotide can bedetermined by methods well known in the art such as, activity assays,Western blots using antibodies capable of specifically binding thepolypeptide, Enzyme-Linked Immuno Sorbent Assay (ELISA),radio-immuno-assays (RIA), immunohistochemistry, immunocytochemistry,immunofluorescence and the like.

Methods of determining the level in the plant of the RNA transcribedfrom the exogenous polynucleotide are well known in the art and include,for example, Northern blot analysis, reverse transcription polymerasechain reaction (RT-PCR) analysis (including quantitative,semi-quantitative or real-time RT-PCR) and RNA-in situ hybridization.

The sequence information and annotations uncovered by the presentteachings can be harnessed in favor of classical breeding. Thus,sub-sequence data of those polynucleotides described above, can be usedas markers for marker assisted selection (MAS), in which a marker isused for indirect selection of a genetic determinant or determinants ofa trait of interest (e.g., biomass, growth rate, oil content, yield,abiotic stress tolerance, water use efficiency, nitrogen use efficiencyand/or fertilizer use efficiency). Nucleic acid data of the presentteachings (DNA or RNA sequence) may contain or be linked to polymorphicsites or genetic markers on the genome such as restriction fragmentlength polymorphism (RFLP), microsatellites and single nucleotidepolymorphism (SNP), DNA fingerprinting (DFP), amplified fragment lengthpolymorphism (AFLP), expression level polymorphism, polymorphism of theencoded polypeptide and any other polymorphism at the DNA or RNAsequence.

Examples of marker assisted selections include, but are not limited to,selection for a morphological trait (e.g., a gene that affects form,coloration, male sterility or resistance such as the presence or absenceof awn, leaf sheath coloration, height, grain color, aroma of rice);selection for a biochemical trait (e.g., a gene that encodes a proteinthat can be extracted and observed; for example, isozymes and storageproteins); selection for a biological trait (e.g., pathogen races orinsect biotypes based on host pathogen or host parasite interaction canbe used as a marker since the genetic constitution of an organism canaffect its susceptibility to pathogens or parasites).

The polynucleotides and polypeptides described hereinabove can be usedin a wide range of economical plants, in a safe and cost effectivemanner.

Plant lines exogenously expressing the polynucleotide or the polypeptideof the invention are screened to identify those that show the greatestincrease of the desired plant trait.

Thus, according to an additional embodiment of the present invention,there is provided a method of evaluating a trait of a plant, the methodcomprising: (a) expressing in a plant or a portion thereof the nucleicacid construct of some embodiments of the invention; and (b) evaluatinga trait of a plant as compared to a wild type plant of the same type(e.g., a plant not transformed with the claimed biomolecules); therebyevaluating the trait of the plant.

According to an aspect of some embodiments of the invention there isprovided a method of producing a crop comprising growing a crop of aplant expressing an exogenous polynucleotide comprising a nucleic acidsequence encoding a polypeptide at least about 80%, at least about 81%,at least about 82%, at least about 83%, at least about 84%, at leastabout 85%, at least about 86%, at least about 87%, at least about 88%,at least about 89%, at least about 90%, at least about 91%, at leastabout 92%, at least about 93%, at least about 94%, at least about 95%,at least about 96%, at least about 97%, at least about 98%, at leastabout 99%, or more say 100% homologous to the amino acid sequenceselected from the group consisting of SEQ ID NOs: 220-366, 5629-9399,9400, 9701-9708, 9753-9795 and 9796, wherein said plant is derived froma plant selected for increased fertilizer use efficiency (e.g., nitrogenuse efficiency), increased oil content, increased yield, increasedgrowth rate, increased biomass, increased vigor, increased fiber yield,increased fiber quality, and/or increased abiotic stress tolerance ascompared to a control plant, thereby producing the crop.

According to an aspect of some embodiments of the invention there isprovided a method of producing a crop comprising growing a crop of aplant expressing an exogenous polynucleotide which comprises a nucleicacid sequence which is at least about 80%, at least about 81%, at leastabout 82%, at least about 83%, at least about 84%, at least about 85%,at least about 86%, at least about 87%, at least about 88%, at leastabout 89%, at least about 90%, at least about 91%, at least about 92%,at least about 93%, at least about 93%, at least about 94%, at leastabout 95%, at least about 96%, at least about 97%, at least about 98%,at least about 99%, e.g., 100% identical to the nucleic acid sequenceselected from the group consisting of SEQ ID NOs: 1-219, 367-5627, 5628,9688-9700, 9709-9751 and 9752, wherein said plant is derived from aplant selected for increased fertilizer use efficiency (e.g., nitrogenuse efficiency), increased oil content, increased yield, increasedgrowth rate, increased biomass, increased vigor, increased fiber yield,increased fiber quality, and/or increased abiotic stress tolerance ascompared to a control plant, thereby producing the crop.

According to an aspect of some embodiments of the invention there isprovided a method of growing a crop comprising seeding seeds and/orplanting plantlets of a plant transformed with the exogenouspolynucleotide of the invention, e.g., the polynucleotide which encodesthe polypeptide of some embodiments of the invention, wherein the plantis derived from plants selected for at least one trait selected from thegroup consisting of increased abiotic stress tolerance, increasednitrogen use efficiency, increased biomass, increased growth rate,increased vigor, increased yield and increased fiber yield or quality ascompared to a non-transformed plant.

According to some embodiments of the invention the method of growing acrop comprising seeding seeds and/or planting plantlets of a planttransformed with an exogenous polynucleotide comprising a nucleic acidsequence encoding a polypeptide at least about 80%, at least about 81%,at least about 82%, at least about 83%, at least about 84%, at leastabout 85%, at least about 86%, at least about 87%, at least about 88%,at least about 89%, at least about 90%, at least about 91%, at leastabout 92%, at least about 93%, at least about 93%, at least about 94%,at least about 95%, at least about 96%, at least about 97%, at leastabout 98%, at least about 99%, e.g., 100% identical to SEQ ID NO:220-366, 5629-9399, 9400, 9701-9708, 9753-9795 or 9796, wherein theplant is derived from plants selected for at least one trait selectedfrom the group consisting of increased abiotic stress tolerance,increased nitrogen use efficiency, increased biomass, increased growthrate, increased vigor, increased yield, increased fiber yield orquality, and increased oil content as compared to a non-transformedplant, thereby growing the crop.

According to some embodiments of the invention the method of growing acrop comprising seeding seeds and/or planting plantlets of a planttransformed with an exogenous polynucleotide comprising the nucleic acidsequence at least about 80%, at least about 81%, at least about 82%, atleast about 83%, at least about 84%, at least about 85%, at least about86%, at least about 87%, at least about 88%, at least about 89%, atleast about 90%, at least about 91%, at least about 92%, at least about93%, at least about 93%, at least about 94%, at least about 95%, atleast about 96%, at least about 97%, at least about 98%, at least about99%, e.g., 100% identical to SEQ ID NO: 1-219, 367-5627, 5628,9688-9700, 9709-9751 or 9752, wherein the plant is derived from plantsselected for at least one trait selected from the group consisting ofincreased abiotic stress tolerance, increased nitrogen use efficiency,increased biomass, increased growth rate, increased vigor, increasedyield, increased fiber yield or quality, and increased oil content ascompared to a non-transformed plant, thereby growing the crop.

The effect of the transgene (the exogenous polynucleotide encoding thepolypeptide) on abiotic stress tolerance can be determined using knownmethods such as detailed below and in the Examples section whichfollows.

Abiotic Stress Tolerance—

Transformed (i.e., expressing the transgene) and non-transformed (wildtype) plants are exposed to an abiotic stress condition, such as waterdeprivation, suboptimal temperature (low temperature, high temperature),nutrient deficiency, nutrient excess, a salt stress condition, osmoticstress, heavy metal toxicity, anaerobiosis, atmospheric pollution and UVirradiation.

Salinity Tolerance Assay—

Transgenic plants with tolerance to high salt concentrations areexpected to exhibit better germination, seedling vigor or growth in highsalt. Salt stress can be effected in many ways such as, for example, byirrigating the plants with a hyperosmotic solution, by cultivating theplants hydroponically in a hyperosmotic growth solution (e.g., Hoaglandsolution), or by culturing the plants in a hyperosmotic growth medium[e.g., 50% Murashige-Skoog medium (MS medium)]. Since different plantsvary considerably in their tolerance to salinity, the salt concentrationin the irrigation water, growth solution, or growth medium can beadjusted according to the specific characteristics of the specific plantcultivar or variety, so as to inflict a mild or moderate effect on thephysiology and/or morphology of the plants (for guidelines as toappropriate concentration see. Bernstein and Kafkafi, Root Growth UnderSalinity Stress In: Plant Roots. The Hidden Half 3rd ed. Waisel Y, EshelA and Kafkafi U. (editors) Marcel Dekker Inc., New York, 2002, andreference therein).

For example, a salinity tolerance test can be performed by irrigatingplants at different developmental stages with increasing concentrationsof sodium chloride (for example 50 mM, 100 mM, 200 mM, 400 mM NaCl)applied from the bottom and from above to ensure even dispersal of salt.Following exposure to the stress condition the plants are frequentlymonitored until substantial physiological and/or morphological effectsappear in wild type plants. Thus, the external phenotypic appearance,degree of wilting and overall success to reach maturity and yieldprogeny are compared between control and transgenic plants.

Quantitative parameters of tolerance measured include, but are notlimited to, the average wet and dry weight, growth rate, leaf size, leafcoverage (overall leaf area), the weight of the seeds yielded, theaverage seed size and the number of seeds produced per plant.Transformed plants not exhibiting substantial physiological and/ormorphological effects, or exhibiting higher biomass than wild-typeplants, are identified as abiotic stress tolerant plants.

Osmotic Tolerance Test—

Osmotic stress assays (including sodium chloride and mannitol assays)are conducted to determine if an osmotic stress phenotype was sodiumchloride-specific or if it was a general osmotic stress relatedphenotype. Plants which are tolerant to osmotic stress may have moretolerance to drought and/or freezing. For salt and osmotic stressgermination experiments, the medium is supplemented for example with 50mM, 100 mM, 200 mM NaCl or 100 mM, 200 mM NaCl, 400 mM mannitol.

Drought Tolerance Assay/Osmoticum Assay—

Tolerance to drought is performed to identify the genes conferringbetter plant survival after acute water deprivation. To analyze whetherthe transgenic plants are more tolerant to drought, an osmotic stressproduced by the non-ionic osmolyte sorbitol in the medium can beperformed. Control and transgenic plants are germinated and grown inplant-agar plates for 4 days, after which they are transferred to platescontaining 500 mM sorbitol. The treatment causes growth retardation,then both control and transgenic plants are compared, by measuring plantweight (wet and dry), yield, and by growth rates measured as time toflowering.

Conversely, soil-based drought screens are performed with plantsoverexpressing the polynucleotides detailed above. Seeds from controlArabidopsis plants, or other transgenic plants overexpressing thepolypeptide of the invention are germinated and transferred to pots.Drought stress is obtained after irrigation is ceased accompanied byplacing the pots on absorbent paper to enhance the soil-drying rate.Transgenic and control plants are compared to each other when themajority of the control plants develop severe wilting. Plants arere-watered after obtaining a significant fraction of the control plantsdisplaying a severe wilting. Plants are ranked comparing to controls foreach of two criteria: tolerance to the drought conditions and recovery(survival) following re-watering.

Cold Stress Tolerance—

To analyze cold stress, mature (25 day old) plants are transferred to 4°C. chambers for 1 or 2 weeks, with constitutive light. Later on plantsare moved back to greenhouse. Two weeks later damages from chillingperiod, resulting in growth retardation and other phenotypes, arecompared between both control and transgenic plants, by measuring plantweight (wet and dry), and by comparing growth rates measured as time toflowering, plant size, yield, and the like.

Heat Stress Tolerance—

Heat stress tolerance is achieved by exposing the plants to temperaturesabove 34° C. for a certain period. Plant tolerance is examined aftertransferring the plants back to 22° C. for recovery and evaluation after5 days relative to internal controls (non-transgenic plants) or plantsnot exposed to neither cold or heat stress.

Water Use Efficiency—

can be determined as the biomass produced per unit transpiration. Toanalyze WUE, leaf relative water content can be measured in control andtransgenic plants. Fresh weight (FW) is immediately recorded; thenleaves are soaked for 8 hours in distilled water at room temperature inthe dark, and the turgid weight (TW) is recorded. Total dry weight (DW)is recorded after drying the leaves at 60° C. to a constant weight.Relative water content (RWC) is calculated according to the followingFormula I:RWC=[(FW−DW)/(TW−DW)]×100  Formula I

Fertilizer Use Efficiency—

To analyze whether the transgenic plants are more responsive tofertilizers, plants are grown in agar plates or pots with a limitedamount of fertilizer, as described, for example, Yanagisawa et al (ProcNatl Acad Sci USA. 2004; 101:7833-8), which is fully incorporated hereinby reference in its entirety. The plants are analyzed for their overallsize, time to flowering, yield, protein content of shoot and/or grain.The parameters checked are the overall size of the mature plant, its wetand dry weight, the weight of the seeds yielded, the average seed sizeand the number of seeds produced per plant. Other parameters that may betested are: the chlorophyll content of leaves (as nitrogen plant statusand the degree of leaf verdure is highly correlated), amino acid and thetotal protein content of the seeds or other plant parts such as leavesor shoots, oil content, etc. Similarly, instead of providing nitrogen atlimiting amounts, phosphate or potassium can be added at increasingconcentrations. Again, the same parameters measured are the same aslisted above. In this way, nitrogen use efficiency (NUE), phosphate useefficiency (PUE) and potassium use efficiency (KUE) are assessed,checking the ability of the transgenic plants to thrive under nutrientrestraining conditions.

Nitrogen Use Efficiency—

To analyze whether the transgenic plants (e.g., Arabidopsis plants) aremore responsive to nitrogen, plant are grown in 0.75-3 mM (nitrogendeficient conditions) or 6-10 mM (optimal nitrogen concentration).Plants are allowed to grow for additional 25 days or until seedproduction. The plants are then analyzed for their overall size, time toflowering, yield, protein content of shoot and/or grain/seed production.The parameters checked can be the overall size of the plant, wet and dryweight, the weight of the seeds yielded, the average seed size and thenumber of seeds produced per plant. Other parameters that may be testedare: the chlorophyll content of leaves (as nitrogen plant status and thedegree of leaf greenness is highly correlated), amino acid and the totalprotein content of the seeds or other plant parts such as leaves orshoots and oil content. Transformed plants not exhibiting substantialphysiological and/or morphological effects, or exhibiting highermeasured parameters levels than wild-type plants, are identified asnitrogen use efficient plants.

Nitrogen Use Efficiency Assay Using Plantlets—

The assay is done according to Yanagisawa-S. et al. with minormodifications (“Metabolic engineering with Dof1 transcription factor inplants: Improved nitrogen assimilation and growth under low-nitrogenconditions” Proc. Natl. Acad. Sci. USA 101, 7833-7838). Briefly,transgenic plants which are grown for 7-10 days in 0.5×MS[Murashige-Skoog] supplemented with a selection agent are transferred totwo nitrogen-limiting conditions: MS media in which the combinednitrogen concentration (NH₄NO₃ and KNO₃) was 0.75 mM (nitrogen deficientconditions) or 6-15 mM (optimal nitrogen concentration). Plants areallowed to grow for additional 30-40 days and then photographed,individually removed from the Agar (the shoot without the roots) andimmediately weighed (fresh weight) for later statistical analysis.Constructs for which only T1 seeds are available are sown on selectivemedia and at least 20 seedlings (each one representing an independenttransformation event) are carefully transferred to the nitrogen-limitingmedia. For constructs for which T2 seeds are available, differenttransformation events are analyzed. Usually, 20 randomly selected plantsfrom each event are transferred to the nitrogen-limiting media allowedto grow for 3-4 additional weeks and individually weighed at the end ofthat period. Transgenic plants are compared to control plants grown inparallel under the same conditions. Mock-transgenic plants expressingthe uidA reporter gene (GUS) under the same promoter or transgenicplants carrying the same promoter but lacking a reporter gene are usedas control.

Nitrogen Determination—

The procedure for N (nitrogen) concentration determination in thestructural parts of the plants involves the potassium persulfatedigestion method to convert organic N to NO₃ ⁻ (Purcell and King 1996Argon. J. 88:111-113, the modified Cd⁻ mediated reduction of NO₃ ⁻ toNO₂ ⁻ (Vodovotz 1996 Biotechniques 20:390-394) and the measurement ofnitrite by the Griess assay (Vodovotz 1996, supra). The absorbancevalues are measured at 550 nm against a standard curve of NaNO₂. Theprocedure is described in details in Samonte et al. 2006 Agron. J.98:168-176.

Germination Tests—

Germination tests compare the percentage of seeds from transgenic plantsthat could complete the germination process to the percentage of seedsfrom control plants that are treated in the same manner. Normalconditions are considered for example, incubations at 22° C. under22-hour light 2-hour dark daily cycles. Evaluation of germination andseedling vigor is conducted between 4 and 14 days after planting. Thebasal media is 50% MS medium (Murashige and Skoog, 1962 Plant Physiology15, 473-497 which is fully incorporated herein by reference).

Germination is checked also at unfavorable conditions such as cold(incubating at temperatures lower than 10° C. instead of 22° C.) orusing seed inhibition solutions that contain high concentrations of anosmolyte such as sorbitol (at concentrations of 50 mM, 100 mM, 200 mM,300 mM, 500 mM, and up to 1000 mM) or applying increasing concentrationsof salt (of 50 mM, 100 mM, 200 mM, 300 mM, 500 mM NaCl).

The effect of the transgene on plant's vigor, growth rate, biomass,yield and/or oil content can be determined using known methods.

Plant Vigor—

The plant vigor can be calculated by the increase in growth parameterssuch as leaf area, fiber length, rosette diameter, plant fresh weightand the like per time.

Growth Rate—

The growth rate can be measured using digital analysis of growingplants. For example, images of plants growing in greenhouse on plotbasis can be captured every 3 days and the rosette area can becalculated by digital analysis. Rosette area growth is calculated usingthe difference of rosette area between days of sampling divided by thedifference in days between samples.

Evaluation of growth rate can be done by measuring plant biomassproduced, rosette area, leaf size or root length per time (can bemeasured in cm² per day of leaf area).

Area Growth Rate can be calculated using Formula II.Area Growth Rate=Regression coefficient of area along timecourse  Formula II:

Thus, the area growth rate units are cm²/day and the length and diametergrowth rate units are cm/day.

Seed Yield—

Evaluation of the seed yield per plant can be done by measuring theamount (weight or size) or quantity (i.e., number) of dry seeds producedand harvested from 8-16 plants and divided by the number of plants.

For example, the total seeds from 8-16 plants can be collected, weightedusing e.g., an analytical balance and the total weight can be divided bythe number of plants. Seed yield per growing area can be calculated inthe same manner while taking into account the growing area given to asingle plant. Increase seed yield per growing area could be achieved byincreasing seed yield per plant, and/or by increasing number of plantscapable of growing in a given area.

In addition, seed yield can be determined via the weight of 1000 seeds.The weight of 1000 seeds can be determined as follows: seeds arescattered on a glass tray and a picture is taken. Each sample isweighted and then using the digital analysis, the number of seeds ineach sample is calculated.

The 1000 seeds weight can be calculated using formula III:1000 Seed Weight=number of seed in sample/sample weight×1000  FormulaIII

The Harvest Index can be calculated using Formula IV.Harvest Index=Average seed yield per plant/Average dry weight  FormulaIV

Grain Protein Concentration—

Grain protein content (g grain protein m⁻²) is estimated as the productof the mass of grain N (g grain N m⁻²) multiplied by the N/proteinconversion ratio of k-5.13 (Mosse 1990, supra). The grain proteinconcentration is estimated as the ratio of grain protein content perunit mass of the grain (g grain protein kg⁻¹ grain).

Fiber Length—

Fiber length can be measured using fibrograph. The fibrograph system wasused to compute length in terms of “Upper Half Mean” length. The upperhalf mean (UHM) is the average length of longer half of the fiberdistribution. The fibrograph measures length in span lengths at a givenpercentage point (Hypertext Transfer Protocol://World Wide Web (dot)cottoninc (dot) com/ClassificationofCotton/?Pg=4#Length).

According to some embodiments of the invention, increased yield of cornmay be manifested as one or more of the following: increase in thenumber of plants per growing area, increase in the number of ears perplant, increase in the number of rows per ear, number of kernels per earrow, kernel weight, thousand kernel weight (1000-weight), earlength/diameter, increase oil content per kernel and increase starchcontent per kernel.

As mentioned, the increase of plant yield can be determined by variousparameters. For example, increased yield of rice may be manifested by anincrease in one or more of the following: number of plants per growingarea, number of panicles per plant, number of spikelets per panicle,number of flowers per panicle, increase in the seed filling rate,increase in thousand kernel weight (1000-weight), increase oil contentper seed, increase starch content per seed, among others. An increase inyield may also result in modified architecture, or may occur because ofmodified architecture.

Similarly, increased yield of soybean may be manifested by an increasein one or more of the following: number of plants per growing area,number of pods per plant, number of seeds per pod, increase in the seedfilling rate, increase in thousand seed weight (1000-weight), reduce podshattering, increase oil content per seed, increase protein content perseed, among others. An increase in yield may also result in modifiedarchitecture, or may occur because of modified architecture.

Increased yield of canola may be manifested by an increase in one ormore of the following: number of plants per growing area, number of podsper plant, number of seeds per pod, increase in the seed filling rate,increase in thousand seed weight (1000-weight), reduce pod shattering,increase oil content per seed, among others. An increase in yield mayalso result in modified architecture, or may occur because of modifiedarchitecture.

Increased yield of cotton may be manifested by an increase in one ormore of the following: number of plants per growing area, number ofbolls per plant, number of seeds per boll, increase in the seed fillingrate, increase in thousand seed weight (1000-weight), increase oilcontent per seed, improve fiber length, fiber strength, among others. Anincrease in yield may also result in modified architecture, or may occurbecause of modified architecture.

Oil Content—

The oil content of a plant can be determined by extraction of the oilfrom the seed or the vegetative portion of the plant. Briefly, lipids(oil) can be removed from the plant (e.g., seed) by grinding the planttissue in the presence of specific solvents (e.g., hexane or petroleumether) and extracting the oil in a continuous extractor. Indirect oilcontent analysis can be carried out using various known methods such asNuclear Magnetic Resonance (NMR) Spectroscopy, which measures theresonance energy absorbed by hydrogen atoms in the liquid state of thesample [See for example, Conway T F, and Earle F R., 1963. Journal ofthe American Oil Chemists' Society: Springer Berlin/Heidelberg. ISSN:0003-021X (Print) 1558-9331 (Online)]; the Near Infrared (NI)Spectroscopy, which utilizes the absorption of near infrared energy(1100-2500 nm) by the sample; and a method described in WO/2001/023884,which is based on extracting oil a solvent, evaporating the solvent in agas stream which forms oil particles, and directing a light into the gasstream and oil particles which forms a detectable reflected light.

Thus, the present invention is of high agricultural value for promotingthe yield of commercially desired crops (e.g., biomass of vegetativeorgan such as poplar wood, or reproductive organ such as number of seedsor seed biomass).

Any of the transgenic plants described hereinabove or parts thereof maybe processed to produce a feed, meal, protein or oil preparation, suchas for ruminant animals.

The transgenic plants described hereinabove, which exhibit an increasedoil content can be used to produce plant oil (by extracting the oil fromthe plant).

The plant oil (including the seed oil and/or the vegetative portion oil)produced according to the method of the invention may be combined with avariety of other ingredients. The specific ingredients included in aproduct are determined according to the intended use. Exemplary productsinclude animal feed, raw material for chemical modification,biodegradable plastic, blended food product, edible oil, biofuel,cooking oil, lubricant, biodiesel, snack food, cosmetics, andfermentation process raw material. Exemplary products to be incorporatedto the plant oil include animal feeds, human food products such asextruded snack foods, breads, as a food binding agent, aquaculturefeeds, fermentable mixtures, food supplements, sport drinks, nutritionalfood bars, multi-vitamin supplements, diet drinks, and cereal foods.

According to some embodiments of the invention, the oil comprises a seedoil.

According to some embodiments of the invention, the oil comprises avegetative portion oil (oil of the vegetative portion of the plant).

According to some embodiments of the invention, the plant cell forms apart of a plant.

According to another embodiment of the present invention, there isprovided a food or feed comprising the plants or a portion thereof ofthe present invention.

As used herein the term “about” refers to +10%.

The terms “comprises”, “comprising”, “includes”, “including”, “having”and their conjugates mean “including but not limited to”.

The term “consisting of” means including and limited to”.

The term “consisting essentially of” means that the composition, methodor structure may include additional ingredients, steps and/or parts, butonly if the additional ingredients, steps and/or parts do not materiallyalter the basic and novel characteristics of the claimed composition,method or structure.

As used herein, the singular form “a”, “an” and “the” include pluralreferences unless the context clearly dictates otherwise. For example,the term “a compound” or “at least one compound” may include a pluralityof compounds, including mixtures thereof.

Throughout this application, various embodiments of this invention maybe presented in a range format. It should be understood that thedescription in range format is merely for convenience and brevity andshould not be construed as an inflexible limitation on the scope of theinvention. Accordingly, the description of a range should be consideredto have specifically disclosed all the possible subranges as well asindividual numerical values within that range. For example, descriptionof a range such as from 1 to 6 should be considered to have specificallydisclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numberswithin that range, for example, 1, 2, 3, 4, 5, and 6. This appliesregardless of the breadth of the range.

Whenever a numerical range is indicated herein, it is meant to includeany cited numeral (fractional or integral) within the indicated range.The phrases “ranging/ranges between” a first indicate number and asecond indicate number and “ranging/ranges from” a first indicate number“to” a second indicate number are used herein interchangeably and aremeant to include the first and second indicated numbers and all thefractional and integral numerals therebetween.

As used herein the term “method” refers to manners, means, techniquesand procedures for accomplishing a given task including, but not limitedto, those manners, means, techniques and procedures either known to, orreadily developed from known manners, means, techniques and proceduresby practitioners of the chemical, pharmacological, biological,biochemical and medical arts.

It is appreciated that certain features of the invention, which are, forclarity, described in the context of separate embodiments, may also beprovided in combination in a single embodiment. Conversely, variousfeatures of the invention, which are, for brevity, described in thecontext of a single embodiment, may also be provided separately or inany suitable subcombination or as suitable in any other describedembodiment of the invention. Certain features described in the contextof various embodiments are not to be considered essential features ofthose embodiments, unless the embodiment is inoperative without thoseelements.

Various embodiments and aspects of the present invention as delineatedhereinabove and as claimed in the claims section below find experimentssupport in the following examples.

EXAMPLES

Reference is now made to the following examples, which together with theabove descriptions illustrate some embodiments of the invention in a nonlimiting fashion.

Generally, the nomenclature used herein and the laboratory proceduresutilized in the present invention include molecular, biochemical,microbiological and recombinant DNA techniques. Such techniques arethoroughly explained in the literature. See, for example, “MolecularCloning: A laboratory Manual” Sambrook et al., (1989); “CurrentProtocols in Molecular Biology” Volumes I-III Ausubel. R. M., ed.(1994); Ausubel et al., “Current Protocols in Molecular Biology”, JohnWiley and Sons, Baltimore, Md. (1989); Perbal, “A Practical Guide toMolecular Cloning”. John Wiley & Sons, New York (1988); Watson et al.,“Recombinant DNA”. Scientific American Books, New York; Birren et al.(eds) “Genome Analysis: A Laboratory Manual Series”, Vols. 1-4, ColdSpring Harbor Laboratory Press, New York (1998); methodologies as setforth in U.S. Pat. Nos. 4,666,828; 4,683,202; 4,801,531; 5,192,659 and5,272,057; “Cell Biology: A Laboratory Handbook”, Volumes I-III Cellis,J. E., ed. (1994): “Current Protocols in Immunology” Volumes I-IIIColigan J. E., ed. (1994): Stites et al. (eds), “Basic and ClinicalImmunology” (8th Edition), Appleton & Lange, Norwalk, Conn. (1994);Mishell and Shiigi (eds), “Selected Methods in Cellular Immunology”, W.H. Freeman and Co., New York (1980); available immunoassays areextensively described in the patent and scientific literature, see, forexample, U.S. Pat. Nos. 3,791,932; 3,839,153; 3,850,752; 3,850,578;3,853,987; 3,867,517; 3,879,262; 3,901,654; 3,935,074; 3,984,533;3,996,345; 4,034,074; 4,098,876; 4,879,219; 5,011,771 and 5,281,521;“Oligonucleotide Synthesis” Gait, M. J., ed. (1984); “Nucleic AcidHybridization” Hames, B. D., and Higgins S. J., eds. (1985);“Transcription and Translation” Hames, B. D., and Higgins S. J., Eds.(1984); “Animal Cell Culture” Freshney. R. I., ed. (1986); “ImmobilizedCells and Enzymes” IRL Press, (1986); “A Practical Guide to MolecularCloning” Perbal, B., (1984) and “Methods in Enzymology” Vol. 1-317,Academic Press; “PCR Protocols: A Guide To Methods And Applications”,Academic Press, San Diego. Calif. (1990); Marshak et al., “Strategiesfor Protein Purification and Characterization—A Laboratory CourseManual” CSHL Press (1996): all of which are incorporated by reference asif fully set forth herein. Other general references are providedthroughout this document. The procedures therein are believed to be wellknown in the art and are provided for the convenience of the reader. Allthe information contained therein is incorporated herein by reference.

General Experimental and Bioinformatics Methods

RNA Extraction—

Tissues growing at various growth conditions (as described below) weresampled and RNA was extracted using TRIzol Reagent from Invitrogen[Hypertext Transfer Protocol://World Wide Web (dot) invitrogen (dot)corn/content (dot)cfm?pageid=469]. Approximately 30-50 mg of tissue wastaken from samples. The weighed tissues were ground using pestle andmortar in liquid nitrogen and resuspended in 500 μl, of TRIzol Reagent.To the homogenized lysate, 100 μl, of chloroform was added followed byprecipitation using isopropanol and two washes with 75% ethanol. The RNAwas eluted in 30 μl of RNase-free water. RNA samples were cleaned upusing Qiagen's RNeasy minikit clean-up protocol as per themanufacturer's protocol (QIAGEN Inc, CA USA). For convenience, eachmicro-array expression information tissue type has received anexpression Set ID.

Correlation Analysis—

was performed for selected genes according to some embodiments of theinvention, in which the characterized parameters (measured parametersaccording to the correlation IDs) were used as “x axis” for correlationwith the tissue transcriptome which was used as the “Y axis”. For eachgene and measured parameter a correlation coefficient “R” was calculated(using Pearson correlation) along with a p-value for the significance ofthe correlation. When the correlation coefficient (R) between the levelsof a gene's expression in a certain tissue and a phenotypic performanceacross ecotypes/variety/hybrid is high in absolute value (between0.5-1), there is an association between the gene (specifically theexpression level of this gene) the phenotypic characteristic (e.g.,improved nitrogen use efficiency, abiotic stress tolerance, yield,growth rate and the like).

Example 1 Bio-Informatics Tools for Identification of Genes whichIncrease Abiotic Stress Tolerance, Yield and Agronomical ImportantTraits in Plants

The present inventors have identified polynucleotides which expressionthereof in plants can increase abiotic stress tolerance (ABST), wateruse efficiency (WUE), yield, fiber yield, fiber quality, oil content,growth rate, vigor, biomass, nitrogen use efficiency (NUE), andfertilizer use efficiency (FUE) such as nitrogen use efficiency (NUE),water use efficiency (WUE) of a plant.

All nucleotide sequence datasets used here were originated from publiclyavailable databases or from performing sequencing using the Solexatechnology (e.g. Barley and Sorghum). Sequence data from 100 differentplant species was introduced into a single, comprehensive database.Other information on gene expression, protein annotation, enzymes andpathways were also incorporated. Major databases used include:

-   -   Genomes    -   Arabidopsis genome [TAIR genome version 6 (Hypertext Transfer        Protocol://World Wide Web (dot) arabidopsis (dot) org/)]    -   Rice genome [IRGSP build 4.0 (Hypertext Transfer Protocol://rgp        (dot) dna (dot) affrc (dot) go (dot) jp/IRGSP/)].    -   Poplar [Populus trichocarpa release 1.1 from JGI (assembly        release v1.0) (Hypertext Transfer Protocol://World Wide Web        (dot) genome (dot) jgi-psf (dot) org/)]    -   Brachypodium [JGI 4× assembly, Hypertext Transfer        Protocol://World Wide Web (dot) brachypodium (dot) org)]    -   Soybean [DOE-JGI SCP, version Glyma0 (Hypertext Transfer        Protocol://World Wide Web (dot) phytozome (dot) net/)]    -   Grape [French-Italian Public Consortium for Grapevine Genome        Characterization grapevine genome (Hypertext Transfer        Protocol://World Wide Web (dot) genoscope (dot) cns (dot) fr/)]    -   Castorbean [TIGR/J Craig Venter Institute 4× assembly        [(Hypertext Transfer Protocol://msc (dot) jcvi (dot)        org/r_communis]    -   Sorghum [DOE-JGI SCP, version Sbi1 [Hypertext Transfer        Protocol://World Wide Web (dot) phytozome (dot) net/)].    -   Partially assembled genome of Maize [Hypertext Transfer        Protocol://maizesequence (dot) org/]    -   Expressed EST and mRNA sequences were extracted from the        following databases:    -   GenBank versions 154, 157, 160, 161, 164, 165, 166 and 168        (Hypertext Transfer Protocol://World Wide Web (dot) ncbi (dot)        nlm (dot) nih (dot) gov/dbEST/)    -   RefSeq (Hypertext Transfer Protocol://World Wide Web (dot) ncbi        (dot) nlm (dot) nih (dot) gov/RefSeq/).    -   TAIR (Hypertext Transfer Protocol://World Wide Web (dot)        arabidopsis (dot) org/).    -   Protein and pathway databases    -   Uniprot [Hypertext Transfer Protocol://World Wide Web (dot)        uniprot (dot) org/].    -   AraCyc [Hypertext Transfer Protocol://World Wide Web (dot)        arabidopsis (dot) org/biocyc/index (dot) jsp].    -   ENZYME [Hypertext Transfer Protocol://expasy (dot) org/enzyme/].    -   Microarray datasets were downloaded from:    -   GEO (Hypertext Transfer Protocol://World Wide        Web.ncbi.nlm.nih.gov/geo/)    -   TAIR (Hypertext Transfer Protocol://World Wide        Web.arabidopsis.org/).    -   Proprietary microarray data (WO2008/122980 and the Examples        section below).    -   QTL and SNPs information    -   Gramene [Hypertext Transfer Protocol://World Wide Web (dot)        gramene (dot) org/qtl/].    -   Panzea [Hypertext Transfer Protocol://World Wide Web (dot)        panzea (dot) org/index (dot) html].

Database Assembly—

was performed to build a wide, rich, reliable annotated and easy toanalyze database comprised of publicly available genomic mRNA, ESTs DNAsequences, data from various crops as well as gene expression, proteinannotation and pathway data QTLs, and other relevant information.

Database assembly is comprised of a toolbox of gene refining,structuring, annotation and analysis tools enabling to construct atailored database for each gene discovery project. Gene refining andstructuring tools enable to reliably detect splice variants andantisense transcripts, generating understanding of various potentialphenotypic outcomes of a single gene. The capabilities of the “LEADS”platform of Compugen LTD for analyzing human genome have been confirmedand accepted by the scientific community [see e.g., “WidespreadAntisense Transcription”. Yelin, et al. (2003) Nature Biotechnology 21,379-85; “Splicing of Alu Sequences”. Lev-Maor, et al. (2003) Science 300(5623), 1288-91; “Computational analysis of alternative splicing usingEST tissue information”. Xie H et al. Genomics 2002], and have beenproven most efficient in plant genomics as well.

EST Clustering and Gene Assembly—

For gene clustering and assembly of organisms with available genomesequence data (arabidopsis, rice, castorbean, grape, brachypodium,poplar, soybean, sorghum) the genomic LEADS version (GANG) was employed.This tool allows most accurate clustering of ESTs and mRNA sequences ongenome, and predicts gene structure as well as alternative splicingevents and anti-sense transcription.

For organisms with no available full genome sequence data, “expressedLEADS” clustering software was applied.

Gene Annotation—

Predicted genes and proteins were annotated as follows: Blast search[Hypertext Transfer Protocol://blast (dot) ncbi (dot) nlm (dot) nih(dot) gov/Blast (dot) cgi] against all plant UniProt [Hypertext TransferProtocol://World Wide Web (dot) uniprot (dot) org/] sequences wasperformed. Open reading frames of each putative transcript were analyzedand longest ORF with higher number of homologues was selected aspredicted protein of the transcript. The predicted proteins wereanalyzed by InterPro [Hypertext Transfer Protocol://World Wide Web (dot)ebi (dot) ac (dot) uk/interpro/].

Blast against proteins from AraCyc and ENZYME databases was used to mapthe predicted transcripts to AraCyc pathways.

Predicted proteins from different species were compared using blastalgorithm [Hypertext Transfer Protocol://World Wide Web (dot) ncbi (dot)nlm (dot) nih (dot) gov/Blast (dot) cgi] to validate the accuracy of thepredicted protein sequence, and for efficient detection of orthologs.

Gene Expression Profiling—

Several data sources were exploited for gene expression profiling,namely microarray data and digital expression profile (see below).According to gene expression profile, a correlation analysis wasperformed to identify genes which are co-regulated under differentdevelopment stages and environmental conditions and associated withdifferent phenotypes.

Publicly available microarray datasets were downloaded from TAIR andNCBI GEO sites, renormalized, and integrated into the database.Expression profiling is one of the most important resource data foridentifying genes important for ABST, increased yield, growth rate,vigor, biomass, oil content. WUE, NUE and FUE of a plant.

A digital expression profile summary was compiled for each clusteraccording to all keywords included in the sequence records comprisingthe cluster. Digital expression, also known as electronic Northern Blot,is a tool that displays virtual expression profile based on the ESTsequences forming the gene cluster. The tool provides the expressionprofile of a cluster in terms of plant anatomy (e.g., the tissue/organin which the gene is expressed), developmental stage (the developmentalstages at which a gene can be found) and profile of treatment (providesthe physiological conditions under which a gene is expressed such asdrought, cold, pathogen infection, etc). Given a random distribution ofESTs in the different clusters, the digital expression provides aprobability value that describes the probability of a cluster having atotal of N ESTs to contain X ESTs from a certain collection oflibraries. For the probability calculations, the following is taken intoconsideration: a) the number of ESTs in the cluster, b) the number ofESTs of the implicated and related libraries, c) the overall number ofESTs available representing the species. Thereby clusters with lowprobability values are highly enriched with ESTs from the group oflibraries of interest indicating a specialized expression.

Recently, the accuracy of this system was demonstrated by Portnoy etal., 2009 (Analysis Of The Melon Fruit Transcriptome Based On 454Pyrosequencing) in: Plant & Animal Genomes XVII Conference, San Diego,Calif. Transcriptomic analysis, based on relative EST abundance in datawas performed by 454 pyrosequencing of cDNA representing mRNA of themelon fruit. Fourteen double strand cDNA samples obtained from twogenotypes, two fruit tissues (flesh and rind) and four developmentalstages were sequenced. GS FLX pyrosequencing (Roche/454 Life Sciences)of non-normalized and purified cDNA samples yielded 1,150,657 expressedsequence tags, that assembled into 67.477 unigenes (32,357 singletonsand 35,120 contigs). Analysis of the data obtained against the CucurbitGenomics Database [Hypertext Transfer Protocol://World Wide Web (dot)icugi (dot) org/j confirmed the accuracy of the sequencing and assembly.Expression patterns of selected genes fitted well their qRT-PCR data.

Example 2 Production of Sorghum Transcriptome and High ThroughputCorrelation Analysis with Yield, NUE, and ABST Related ParametersMeasured in Fields Using 44K Sorguhm Oligonucleotide Micro-Arrays

In order to produce a high throughput correlation analysis between plantphenotype and gene expression level, the present inventors utilized asorghum oligonucleotide micro-array, produced by Agilent Technologies[Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent(dot) com/Scripts/PDS (dot) asp?1Page=50879]. The array oligonucleotiderepresents about 44,000 sorghum genes and transcripts. In order todefine correlations between the levels of RNA expression with ABST,yield and NUE components or vigor related parameters, various plantcharacteristics of 17 different sorghum hybrids were analyzed. Amongthem, 10 hybrids encompassing the observed variance were selected forRNA expression analysis. The correlation between the RNA levels and thecharacterized parameters was analyzed using Pearson correlation test[Hypertext Transfer Protocol://World Wide Web (dot) davidmlane (dot)com/hyperstat/A34739 (dot) html].

1. Correlation of Sorghum Varieties Grown Under Regular GrowthConditions, Severe Drought Conditions and Low Nitrogen Conditions

Experimental Procedures

17 Sorghum varieties were grown in 3 repetitive plots, in field.Briefly, the growing protocol was as follows:

1. Regular Growth Conditions:

sorghum plants were grown in the field using commercial fertilizationand irrigation protocols, which include 370 m³ water per dunam (i.e.,1000 m²) per entire growth period and fertilization of 14 units of URAN®21% (Nitrogen Fertilizer Solution; PCS Sales. Northbrook. Ill., USA)(normal growth conditions).

2. Drought Conditions:

sorghum seeds were sown in soil and grown under normal condition untilaround 35 days from sowing, around stage V8 (eight green leaves arefully expanded, booting not started yet). At this point, irrigation wasstopped, and severe drought stress was developed.

3. Low Nitrogen Fertilization Conditions:

sorghum plants were fertilized with 50% less amount of nitrogen in thefield than the amount of nitrogen applied in the regular growthtreatment. All the fertilizer was applied before flowering.

Analyzed Sorghum Tissues—

All 10 selected Sorghum hybrids were sampled per each treatment. Tissues[Flag leaf, Flower meristem and Flower] from plants growing under normalconditions, severe drought stress and low nitrogen conditions weresampled and RNA was extracted as described above. Each micro-arrayexpression information tissue type has received a Set ID as summarizedin Table 1 below.

TABLE 1 Sorghum transcriptome expression sets in field experimentsExpression Set Set ID Sorghum Field/Flag Leaf Drought 1 SorghumField/Flag Leaf NUE 2 Sorghum Field/Flag Leaf Normal 3 SorghumField/Flower Meristem Drought 4 Sorghum Field/Flower Meristem NUE 5Sorghum Field/Flower Meristem Normal 6 Sorghum Field/Flower Drought 7Sorghum Field/Flower NUE 8 Sorghum Field/Flower Normal 9 Provided arethe sorghum transcriptome expression set 1-9.

The following parameters were collected using digital imaging system:

Average Grain Area (cm²)—

At the end of the growing period the grains were separated from thePlant ‘Head’. Samples of ˜200 grains each were weighted, photographedand images were processed using the below described image processingsystem. The grain area was measured from those images and was divided bythe number of grains.

Average Grain Length (cm)—

At the end of the growing period the grains were separated from thePlant ‘Head’. A sample of ˜200 grains were weighted, photographed andimages were processed using the below described image processing system.The sum of grain lengths (longest axis) was measured from those imagesand was divided by the number of grains.

Head Average Area (cm²)—

At the end of the growing period 5 ‘Heads’ were, photographed and imageswere processed using the below described image processing system. The‘Head’ area was measured from those images and was divided by the numberof ‘Heads’.

Head Average Length (cm)—

At the end of the growing period 5 ‘Heads’ were, photographed and imageswere processed using the below described image processing system. The‘Head’ length (longest axis) was measured from those images and wasdivided by the number of ‘Heads’.

An image processing system was used, which consists of a personaldesktop computer (Intel P4 3.0 GHz processor) and a public domainprogram—ImageJ 1.37, Java based image processing software, which wasdeveloped at the U.S. National Institutes of Health and is freelyavailable on the internet at Hypertext Transfer Protocol://rsbweb (dot)nih (dot) gov/. Images were captured in resolution of 10 Mega Pixels(3888×2592 pixels) and stored in a low compression JPEG (JointPhotographic Experts Group standard) format. Next, image processingoutput data for seed area and seed length was saved to text files andanalyzed using the JMP statistical analysis software (SAS institute).

Additional parameters were collected either by sampling 5 plants perplot or by measuring the parameter across all the plants within theplot.

Total Seed Weight Per Head (Gr.)—

At the end of the experiment (plant ‘Heads’) heads from plots withinblocks A-C were collected. 5 heads were separately threshed and grainswere weighted, all additional heads were threshed together and weightedas well. The average grain weight per head was calculated by dividingthe total grain weight by number of total heads per plot (based onplot). In case of 5 heads, the total grains weight of 5 heads wasdivided by 5.

FW Head Per Plant Gram—

At the end of the experiment (when heads were harvested) total heads and5 selected heads per plots within blocks A-C were collected separately.The heads (total and 5) were weighted (Gr.) separately, and the averagefresh weight per plant was calculated for total (FW Head/Plant gr. basedon plot) and for 5 (FW Head/Plant gr. based on 5 plants) heads.

Plant Height—

Plants were characterized for height during growing period at 5 timepoints. In each measure, plants were measured for their height using ameasuring tape. Height was measured from ground level to top of thelongest leaf.

Plant Leaf Number—

Plants were characterized for leaf number during growing period at 5time points. In each measure, plants were measured for their leaf numberby counting all the leaves of 3 selected plants per plot.

Growth Rate—

was calculated using Formulas V and VI.Growth rate of plant height=Regression coefficient of plant height alongtime course.  Formula VGrowth rate of plant leaf number=Regression coefficient of plant leafnumber along time course.  Formula VI

SPAD—

Chlorophyll content was determined using a Minolta SPAD 502 chlorophyllmeter and measurement was performed 64 days post sowing. SPAD meterreadings were done on young fully developed leaf. Three measurements perleaf were taken per plot.

Vegetative Dry Weight and Heads—

At the end of the experiment (when inflorescence were dry) allinflorescence and vegetative material from plots within blocks A-C werecollected. The biomass and heads weight of each plot was separated,measured and divided by the number of heads.

Dry weight=total weight of the vegetative portion above ground(excluding roots) after drying at 70° C. in oven for 48 hours;

Harvest Index (HI) (Sorghum)—

The harvest index was calculated using Formula VII.Harvest Index=Average grain dry weight per Head/(Average vegetative dryweight per Head+Average Head dry weight)  Formula VII

Harvest Index for Sorghum*(* when the plants were not dried) wascalculated using Formula VIII as follows:Harvest Index for Sorghum*=FW(fresh weight)Heads/(FW Heads+FWPlants)  Formula VIII

The total fresh weight of heads and their respective plant biomass wasmeasured at the harvest day. The heads weight was divided by the sum ofweights of heads and plants.

Data parameters collected are summarized in Table 2, herein below

TABLE 2 Sorghum correlated parameters (vectors) Correlated parameterwith Correlation ID Average Grain Area (cm²), Drought 1 Average GrainArea (cm²), Low N 2 Average Grain Area (cm²), Normal 3 FW-Head/Plant gr.(based on plot), Drought 4 FW-Head/Plant gr. (based on plot), Low N 5FW-Head/Plant gr. (based on plot), Normal 6 FW-Head/Plant gr, (based on5 plants), Low N 7 FW-Head/Plant gr. based on 5 plants), Normal 8 FWHeads/(FW Heads + FW Plants)(all plot), Drought 9 FW Heads/(FW Heads +FW Plants)(all plot), Low N 10 FW Heads/(FW Heads + FW Pla.nts)(allplot), Normal 11 FW/Plant gr. (based on plot), Drought 12 FW/Plant gr.(based on plot), Low N 13 FW/Plant gr. (based on plot), Normal 14 FinalPlant Height (cm), Drought 15 Final Plant Height (cm), Low N 16 FinalPlant Height (cm), Normal 17 Head Average Area (cm²), Drought 18 HeadAverage Area (cm²), Low N 19 Head Average Area (cm²), Normal 20 HeadAverage Length (cm), Drought 21 Head Average Length (cm), Low N 22 HeadAverage Length (cm), Normal 23 Head Average Perimeter (cm), Drought 24Head Average Perimeter (cm), Low N 25 Head Average Perimeter (cm),Normal 26 Head Average Width (cm), Drought 27 Head Average Width (cm),Low N 28 Head Average Width (cm), Normal 29 Leaf SPAD 64 DPS (Days PostSowing), Drought 30 Leaf SPAD 64 DPS (Days Post Sowing), Low N 31 LeafSPAD 64 DPS (Days Post Sowing), Normal 32 Lower Ratio Average GrainArea, Low N 33 Lower Ratio Average Grain Area, Normal 34 Lower RatioAverage Grain Length, Low N 35 Lower Ratio Average Grain Length, Normal36 Lower Ratio Average Grain Perimeter, Low N 37 Lower Ratio AverageGrain Perimeter, Normal 38 Lower Ratio Average Grain Width, Low N 39Lower Ratio Average Grain Width, Normal 40 Total grain weight/Head(based on plot) gr., Low N 41 Total grain weight/Head gr. (based on 5heads), Low N 42 Total grain weight/Head gr. (based on 5 heads), Normal43 Total grain weight/Head. gr. based. on plot), Normal 44 Total grainweight Head gr., (based on plot) Drought 45 Upper Ratio Average GrainArea, Drought 46 Upper Ratio Average Grain Area, Low N 47 Upper RatioAverage Grain Area, Normal 48 [Grain Yield + plant biomass/SPAD 64 DPS],Normal 49 [Grain Yield + plant biomass/SPAD 64 DPS], Low N 50 [Grainyield/SPAD 64 DPS], Low N 51 [Grain yield/SPAD 64 DPS], Normal 52 [Plantbiomass (FW)/SPAD 64 DPS], Drought 53 [Plant biomass (FW)/SPAD 64 DPS],Low N 54 [Plant biomass (FW)/SPAD 64 DPS], Normal 55 Provided are theSorghum correlated parameters (vectors). “DW” = Dry Weight; (5I)” =Average of five Inflorescences; “FW” = Fresh Weight; “gr.” = grams; “cm”= centimeter; “SPAD” = chlorophyll levels.

Experimental Results

Normal Growth Condition (for Parameters 1-55)

16 different sorghum varieties were grown and characterized for 55parameters as described above. The average for each of the measuredparameter was calculated using the JMP software and values aresummarized in Tables 3-8 below. Subsequent correlation analysis betweenthe various transcriptome sets (Table 1) and the average parameters, wasconducted. Follow, results were integrated to the database.

TABLE 3 Sorghum accessions, measured parameters under normal growthconditions Ecotype/ Treatment Line-1 Line-2 Line-3 Line-4 Line-5 Line-6Line-7 Line-8 1 0.10 0.11 0.11 0.09 0.09 0.11 2 0.11 0.11 0.14 0.12 0.140.13 0.12 0.12 3 0.10 0.11 0.13 0.13 0.14 0.14 0.11 0.11 4 154.90 122.02130.51 241.11 69.03 186.41 62.11 39.02 5 214.78 205.05 73.49 122.96153.07 93.23 134.11 77.43 6 175.15 223.49 56.40 111.62 67.34 66.90126.18 107.74 7 388.00 428.67 297.67 280.00 208.33 303.67 436.00 376.338 406.50 518.00 148.00 423.00 92.00 101.33 423.50 386.50 9 0.42 0.470.42 0.37 0.23 0.31 0.41 0.44 10 0.51 0.51 0.17 0.39 0.21 0.19 0.48 0.3711 0.51 0.51 0.12 0.26 0.12 0.18 0.46 0.43 12 207.99 138.02 255.41402.22 233.55 391.75 89.31 50.61 13 204.78 199.64 340.51 240.60 537.78359.40 149.20 129.06 14 162.56 212.59 334.83 313.46 462.28 318.26 151.13137.60 15 89.40 75.73 92.10 94.30 150.80 110.73 99.20 84.00 16 104.0080.93 204.73 125.40 225.40 208.07 121.40 100.27 17 95.25 79.20 197.85234.20 189.40 194.67 117.25 92.80 18 83.14 107.79 88.68 135.91 90.76123.95 86.06 85.20 19 96.24 214.72 98.59 182.83 119.64 110.19 172.3684.81 20 120.14 167.60 85.14 157.26 104.00 102.48 168.54 109.32 21 21.6321.94 21.57 22.01 20.99 28.60 21.35 20.81 22 23.22 25.58 20.93 28.4324.32 22.63 32.11 20.38 23 25.58 26.84 21.02 26.84 23.14 21.82 31.3323.18 24 52.78 64.49 56.59 64.37 53.21 71.66 55.61 52.96 25 56.32 79.2053.25 76.21 67.27 59.49 79.28 51.52 26 61.22 67.90 56.26 65.38 67.4667.46 74.35 56.16 27 4.83 6.31 5.16 7.78 5.28 5.49 5.04 5.07 28 5.2610.41 5.93 8.25 6.19 6.12 6.80 5.25 29 5.97 7.92 4.87 7.43 5.58 5.886.78 5.99 30 40.58 40.88 45.01 42.30 45.24 40.56 44.80 45.07 31 38.3338.98 42.33 40.90 43.15 39.85 42.68 43.31 32 43.01 . 43.26 44.74 45.7641.61 45.21 45.14 33 0.82 0.77 0.81 0.79 0.78 0.80 0.83 0.79 34 0.830.74 0.78 0.80 0.70 0.70 0.83 0.81 35 0.91 0.90 0.92 0.90 0.91 0.93 0.920.89 36 0.91 0.88 0.92 0.91 0.89 0.88 0.91 0.90 37 0.90 0.88 0.92 0.900.92 0.92 0.92 0.89 38 0.91 0.87 0.91 0.95 0.90 0.91 0.91 0.91 39 0.900.85 0.89 0.88 0.86 0.87 0.91 0.89 40 0.91 0.83 0.85 0.87 0.79 0.80 0.900.89 41 25.95 30.57 19.37 35.62 25.18 22.18 49.96 27.48 42 50.27 50.9336.13 73.10 37.87 36.40 71.67 35.00 43 47.40 46.30 28.37 70.40 32.1549.23 63.45 44.45 44 31.12 26.35 18.72 38.38 26.67 28.84 47.67 31.00 4521.11 16.77 9.19 104.44 3.24 22.00 9.97 18.58 46 1.31 1.19 1.29 1.461.21 1.21 47 1.18 1.31 1.11 1.21 1.19 1.18 1.16 1.23 48 1.22 1.30 1.131.14 1.16 1.15 1.19 1.23 49 4.50 8.17 7.87 10.68 8.34 4.40 3.74 4.83 506.02 5.91 8.50 6.75 13.05 9.58 4.67 3.61 51 0.68 0.78 0.46 0.87 0.580.56 1.17 0.63 52 3.78 7.74 7.01 10.10 7.65 3.34 3.05 3.90 53 5.13 3.385.67 9.51 5.16 9.66 1.99 1.12 54 5.34 5.12 8.05 5.88 12.46 9.02 3.502.98 55 0.72 0.43 0.86 0.58 0.69 1.05 0.69 0.93 Provided are themeasured parameters under 50% irrigation conditions of Sorghumaccessions (Seed ID) according to the Correlation (Corr.) ID numbers(described in Table 2 above).

TABLE 4 Sorghum accessions, addition measured parameters under normalgrowth conditions Ecotype/ Treatment Line-9 Line-10 Line-11 Line-12Line-13 Line-14 Line-15 Line-16 Line-17 2 0.12 0.13 0.13 0.12 0.12 0.110.11 0.12 0.11 3 0.10 0.12 0.12 0.11 0.12 0.11 0.10 0.11 0.11 4 58.9476.37 33.47 42.20 41.53 131.67 60.84 44.31 185.44 5 129.63 99.83 76.9584.25 92.24 138.83 113.32 95.50 129.49 6 123.86 102.75 82.33 77.59 91.17150.44 109.10 107.58 130.88 7 474.67 437.67 383.00 375.00 425.00 434.00408.67 378.50 432.00 8 409.50 328.95 391.00 435.75 429.50 441.00 415.75429.50 428.50 9 0.40 0.44 0.47 0.47 0.48 0.35 0.35 0.23 0.11 10 0.420.44 0.43 0.39 0.44 0.44 0.44 0.43 0.42 11 0.42 0.44 0.46 0.45 0.45 0.510.46 0.44 0.39 12 87.02 120.43 37.21 48.18 44.20 231.60 116.01 123.08342.50 13 178.71 124.27 101.33 132.12 117.90 176.99 143.67 126.98 180.4514 167.98 128.97 97.62 99.32 112.24 157.42 130.55 135.66 209.21 15 99.0092.20 81.93 98.80 86.47 99.60 83.00 83.53 92.30 16 121.13 94.53 110.00115.07 104.73 173.67 115.60 138.80 144.40 17 112.65 97.50 98.00 100.00105.60 151.15 117.10 124.45 126.50 18 113.10 100.79 80.41 126.89 86.4192.29 77.89 76.93 19 156.25 136.71 137.70 96.54 158.19 163.95 138.39135.46 165.64 20 135.13 169.03 156.10 112.14 154.74 171.70 168.51 162.51170.46 21 24.68 24.28 21.95 24.98 19.49 20.42 16.81 18.88 22 26.69 26.3125.43 23.11 27.87 28.88 27.64 25.52 30.33 23 25.70 28.82 28.13 22.9728.09 30.00 30.54 27.17 29.26 24 69.83 65.14 55.27 69.06 53.32 56.2949.12 51.88 75 69.88 66.17 67.37 57.90 70.61 73.76 66.87 65.40 75.97 2661.64 71.40 68.56 56.44 67.79 71.54 78.94 67.03 74.11 27 5.77 5.37 4.666.35 5.58 5.76 5.86 5.10 28 7.52 6.59 6.85 5.32 7.25 7.19 6.27 6.57 6.8229 6.62 7.42 6.98 6.19 7.02 7.18 7.00 7.39 7.35 30 40.65 45.43 42.5844.18 44.60 42.41 43.25 40.30 40.75 31 39.01 42.71 40.08 43.98 45.4444.75 42.58 43.81 46.73 32 43.03 45.59 44.83 45.33 46.54 43.99 45.0945.14 43.13 33 0.81 0.77 0.74 0.80 0.79 0.82 0.80 0.81 0.81 34 0.84 0.790.77 0.80 0.81 0.82 0.81 0.82 0.82 35 0.90 0.91 0.89 0.90 0.89 0.91 0.890.89 0.90 36 0.92 0.92 0.89 0.91 0.91 0.91 0.90 0.90 0.91 37 0.90 0.910.89 0.90 0.90 0.91 0.89 0.90 0.90 38 0.92 0.93 0.91 0.92 0.90 0.91 0.900.91 0.91 39 0.90 0.86 0.84 0.90 0.89 0.91 0.90 0.90 0.90 40 0.91 0.850.86 0.88 0.90 0.90 0.91 0.90 0.90 41 51.12 36.84 29.45 26.70 29.4251.12 37.04 39.85 41.78 42 76.73 57.58 42.93 36.47 68.60 71.80 49.2743.87 52.07 43 56.65 60.00 45.45 58.19 70.60 70.10 53.95 59.87 52.65 4439.99 38.36 32.10 32.69 32.79 51.53 35.71 38.31 42.44 45 29.27 10.4514.77 12.86 18.24 11.60 18.65 16.36 47 1.17 1.22 1.24 1.19 1.23 1.161.34 1.21 1.21 48 1.25 1.24 1.32 1.22 1.18 1.18 1.22 1.25 1.22 49 3.672.89 2.91 3.12 4.75 3.69 3.85 5.84 50 5.89 3.77 3.26 3.61 3.24 5.10 4.253.81 4.76 51 1.31 0.86 0.73 0.61 0.65 1.14 0.87 0.91 0.89 52 2.83 2.182.19 2.41 3.58 2.90 3.01 4.85 53 2.14 2.65 0.87 1.09 0.99 5.46 2.68 3.058.40 54 4.58 2.91 2.53 3.00 2.60 3.96 3.38 2.90 3.86 55 0.84 0.72 0.720.70 1.17 0.79 0.85 0.98 Provided are the measured parameters undernormal growth conditions of Sorghum accessions (Seed ID) according tothe Correlation (Corr.) ID numbers (described in Table 2 above).

TABLE 5 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance of maintenance of performance under drought conditionsacross sorghum varieties Exp. Corr. Exp. Corr. Gene Name R P value setSet ID Gene Name R P value set Set ID LYM208_H8 0.90 3.78E−04 6 17LYM208_H8 0.91 2.36E−04 6 4 LYM208_H8 0.94 7.14E−05 4 53 LYM208_H8 0.851.92E−03 4 4 LYM208_H8 0.94 4.98E−05 4 12 WYM72 0.76 1.12E−02 3 17 WYM720.81 4.58E−03 3 44 WYM74 0.92 1.95E−04 6 52 WYM74 0.70 2.37E−02 6 14WYM74 0.90 4.28E−04 6 49 WYM74 0.86 1.58E−03 3 3 WYM76 0.76 1.12E−02 923 WYM76 0.80 5 .51E−03 9 44 WYM77 0.83 3.19E−03 6 3 WYM77 0.75 1.20E−029 44 WYM77 0.76 1.15E−02 9 43 WYM77 0.74 1.44E−02 8 41 WYM77 0.833.10E−03 8 35 WYM77 0.74 1.38E−02 8 42 WYM77 0.78 7.20E−03 8 51 WYM770.74 7.07E−04 8 37 WYM77 0.72 1.92E−02 5 2 WYM77 0.78 8.44E−03 3 32WYM77 0.78 8.15E−03 3 40 WYM77 0.84 4.46E−03 3 55 WYM77 0.70 2.41E−02 334 WYM77 0.80 5.42E−03 7 15 WYM79 0.86 1.24E−03 6 48 WYM79 0.75 1.29E−029 3 WYM79 0.78 8.15E−03 3 17 WYM79 0.78 7.44E−03 3 44 WYM79 0.751.28E−02 3 43 WYM80 0.76 1.06E−02 9 17 WYM80 0.74 1.49E−02 9 40 WYM800.84 2.35E−03 9 44 WYM80 0.81 4.72E−03 9 36 WYM80 0.79 6.65E−03 9 34WYM80 0.72 2.00E−02 2 7 WYM80 0.79 7.07E−03 2 41 WYM80 0.80 4.98E−03 235 WYM80 0.79 6.12E−03 2 42 WYM80 0.83 3.12E−03 2 51 WYM80 0.78 7.62E−032 37 WYM80 0.84 2.61E−03 4 53 WYM80 0.72 2.00E−02 4 4 WYM80 0.842.40E−03 4 12 WYM80 0.84 2.48E−03 8 33 WYM80 0.71 2.18E−02 8 50 WYM800.71 2.25E−02 8 39 WYM80 0.91 2.17E−04 8 35 WYM80 0.71 2.26E−02 5 19WYM80 0.77 9.78E−03 5 28 WYM80 0.75 2.09E−02 7 18 WYM80 0.82 6.38E−03 727 WYM81 0.72 1.95E−02 4 30 WYM81 0.78 7.16E−03 8 16 WYM81 0.77 9.25E−033 17 WYM81 0.75 1.28E−02 3 43 WYM83 0.75 1.17E−02 9 43 WYM83 0.779.91E−03 2 31 WYM83 0.72 1.81E−02 2 16 WYM83 0.78 7.80E−03 8 33 WYM830.94 5.34E−05 8 35 WYM83 0.73 1.56E−02 8 42 WYM83 0.86 1.25E−03 8 37WYM83 0.71 2.11E−02 3 17 WYM83 0.74 1.37E−02 3 44 Correlations (R)between the expression level of the genes in various tissues and thephenotypic performance. Corr. ID-correlation set ID according to thecorrelated parameters Table 2 above. Exp. Set-Expression set. R =Pearson correlation coefficient; P = p value.

Example 3 Production of Maize Transcriptome and High ThroughputCorrelation Analysis with Yield and NUE Related Parameters Using 44KMaize Oligonucleotide Micro-Arrays

In order to produce a high throughput correlation analysis between plantphenotype and gene expression level, the present inventors utilized amaize oligonucleotide micro-array, produced by Agilent Technologies[Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent(dot) com/Scripts/PDS (dot) asp?1Page=50879]. The array oligonucleotiderepresents about 44,000 maize genes and transcripts. In order to definecorrelations between the levels of RNA expression with yield and NUEcomponents or vigor related parameters, various plant characteristics of12 different maize hybrids were analyzed. Among them, 10 hybridsencompassing the observed variance were selected for RNA expressionanalysis. The correlation between the RNA levels and the characterizedparameters was analyzed using Pearson correlation test [HypertextTransfer Protocol://World Wide Web (dot) davidmlane (dot)com/hyperstat/A34739 (dot) html].

Correlation of Maize Hybrids Across Ecotypes Grown Under Regular GrowthConditions

Experimental Procedures

12 Maize hybrids were grown in 3 repetitive plots, in field. Maize seedswere planted and plants were grown in the field using commercialfertilization and irrigation protocols. In order to define correlationsbetween the levels of RNA expression with NUE and yield components orvigor related parameters, the 12 different maize hybrids were analyzed.Among them, 10 hybrids encompassing the observed variance were selectedfor RNA expression analysis. The correlation between the RNA levels andthe characterized parameters was analyzed using Pearson correlation test[Hypertext Transfer Protocol://World Wide Web (dot) davidmlane (dot)com/hyperstat/A34739 (dot) html].

Analyzed Maize Tissues—

All 10 selected maize hybrids were sample per each treatment. Planttissues [Flag leaf. Flower meristem. Grain, Cobs. Internodes] growingunder Normal conditions were sampled and RNA was extracted as describedabove. Each micro-array expression information tissue type has receiveda Set ID as summarized in Table 6 below.

TABLE 6 Maize transcriptome expression sets Expression Set Set ID Maizefield/Normal/Leaf 1 Maize field/Normal/Grain 2 Maize field/Normal/Graindistal 3 Maize field/Normal/Grain basal 4 Maize field/Normal/Internodelower 5 Maize field/Normal/Internode upper 6 Provided are the maizetranscriptome expression sets.

The following parameters were collected using digital imaging system:

Grain Area (cm²)—

At the end of the growing period the grains were separated from the ear.A sample of ˜200 grains were weight, photographed and images wereprocessed using the below described image processing system. The grainarea was measured from those images and was divided by the number ofgrains.

Grain Length and Grain Width (cm)—

At the end of the growing period the grains were separated from the ear.A sample of ˜200 grains were weighted, photographed and images wereprocessed using the below described image processing system. The sum ofgrain lengths/or width (longest axis) was measured from those images andwas divided by the number of grains.

Ear Area (cm²)—

At the end of the growing period 5 ears were, photographed and imageswere processed using the below described image processing system. TheEar area was measured from those images and was divided by the number ofEars.

Ear Length and Ear Width (cm)—

At the end of the growing period 5 ears were, photographed and imageswere processed using the below described image processing system. TheEar length and width (longest axis) was measured from those images andwas divided by the number of ears.

The image processing system was used, which consists of a personaldesktop computer (Intel P4 3.0 GHz processor) and a public domainprogram—ImageJ 1.37, Java based image processing software, which wasdeveloped at the U.S. National Institutes of Health and is freelyavailable on the internet at Hypertext Transfer Protocol://rsbweb (dot)nih (dot) gov/. Images were captured in resolution of 10 Mega Pixels(3888×2592 pixels) and stored in a low compression JPEG (JointPhotographic Experts Group standard) format. Next, image processingoutput data for seed area and seed length was saved to text files andanalyzed using the JMP statistical analysis software (SAS institute).

Additional parameters were collected either by sampling 6 plants perplot or by measuring the parameter across all the plants within theplot.

Normalized Grain Weight Per Plant (Gr.)—

At the end of the experiment all ears from plots within blocks A-C werecollected. 6 ears were separately threshed and grains were weighted, alladditional ears were threshed together and weighted as well. The averagegrain weight per ear was calculated by dividing the total grain weightby number of total ears per plot (based on plot). In case of 6 ears, thetotal grains weight of 6 ears was divided by 6.

Ear FW (Gr.)—

At the end of the experiment (when ears were harvested) total and 6selected ears per plots within blocks A-C were collected separately. Theplants with (total and 6) were weighted (Gr.) separately and the averageear per plant was calculated for total (Ear FW per plot) and for 6 (EarFW per plant).

Plant Height and Ear Height—

Plants were characterized for height at harvesting. In each measure, 6plants were measured for their height using a measuring tape. Height wasmeasured from ground level to top of the plant below the tassel. Earheight was measured from the ground level to the place were the main earis located

Leaf Number Per Plant—

Plants were characterized for leaf number during growing period at 5time points. In each measure, plants were measured for their leaf numberby counting all the leaves of 3 selected plants per plot.

The growth rate of leaf number was calculated using Formula VI asindicated above (Growth rate of plant leaf number=Regression coefficientof plant leaf number along time course).Vegetative area growth rate=Regression coefficient of vegetative areaalong time course.  Formula IX—Growth Rate of vegetative area

SPAD—

Chlorophyll content was determined using a Minolta SPAD 502 chlorophyllmeter and measurement was performed 64 days post sowing. SPAD meterreadings were done on young fully developed leaf. Three measurements perleaf were taken per plot. Data were taken after 46 and 54 days aftersowing (DPS)

Dry Weight Per Plant—

At the end of the experiment (when inflorescence were dry) allvegetative material from plots within blocks A-C were collected.

Dry weight=total weight of the vegetative portion above ground(excluding roots) after drying at 70° C. in oven for 48 hours;

Harvest Index (HI) (Maize)—

The harvest index was calculated using Formula X.Harvest Index=Average grain dry weight per Ear/(Average vegetative dryweight per Ear+Average Ear dry weight).  Formula X

Percent Filled Ear [%]—

it was calculated as the percentage of the Ear area with grains out ofthe total ear.

Cob diameter [cm]—

The diameter of the cob without grains was measured using a ruler.

Kernel Row Number Per Ear—

The number of rows in each ear was counted.

Experimental Results

12 different maize hybrids were grown and characterized for differentparameters (Table 7). The average for each of the measured parameter wascalculated using the JMP software (Tables 8-9) and a subsequentcorrelation analysis was performed. Results were then integrated to thedatabase.

TABLE 7 Maize correlated parameters (vectors) Correlated parameter withCorrelation ID Cob Diameter-mm 1 Ear FW per Plant-gr-based on 6 2 EarLength-cm 3 FW per Plant-gr 4 Filled Ears per Plant 5 Growth Rate LeafNum 6 Kernel Row Number per Ear 7 LAI 8 Normalized Grain Weight Der 9plant-gr-based on all Percent Filled Ear Length 10 Plant Height 31DPS-cm11 Stalk Diameter Below Ear-min 12 Stalk Diameter Lowest Internode-mm 13Stalk Width 40DPS-mm 14 Tillers Num per Plant 15 Provided are the maizecorrelated parameters (vectors). “FW” = Fresh Weight; “gr.” = grams;“LAI” = leaf area index; “cm” = centimeter; “SPAD” = chlorophyll levels.

Experimental Results

Six maize accessions were grown, and characterized for parameters, asdescribed above. The average for each parameter was calculated using theJMP software, and values are summarized in Table 8 below. Subsequentcorrelation between the various transcriptome sets for all or sub set oflines was done by the bioinformatics unit and results were integratedinto the database.

TABLE 8 Measured parameters in Maize accessions under normal conditionsEcotype/ Treatment Line-1 Line-2 Line-3 Line-4 Line-5 Line-6 1 26.0225.47 25.86 25.28 24.88 27.44 2 256.21 251.92 275.11 226.24 198.30344.76 3 22.50 21.21 22.33 20.78 19.90 23.39 4 421.94 258.75 342.50326.66 223.06 560.83 5 1.06 1.11 1.11 1.00 1.00 1.56 6 0.16 0.20 0.220.20 0.21 0.18 7 15.03 15.06 14.95 14.42 14.72 15.25 8 78.96 90.84 96.42124.43 140.71 42.82 9 156.07 181.81 166.84 104.15 86.27 222.40 10 89.1989.80 91.09 87.83 84.58 91.93 11 162.72 170.78 168.33 171.25 165.11145.11 12 18.42 18.76 17.84 16.28 14.14 19.98 13 26.45 18.71 25.09 22.7519.38 28.37 14 2.68 2.53 2.18 2.30 2.18 2.96 15 0.50 0.58 0.36 0.06 0.002.00 Provided are the values of each of the parameters (as describedabove) measured in maize accessions (Seed ID) under regular growthconditions. Growth conditions are specified in the experimentalprocedure section.

TABLE 9 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance of maintenance of performance under drought conditionsacross maize lines Exp. Corr. Exp. Corr. Gene Name R P value set Set IDGene Name R P value set Set ID LAB278_H0 0.76 8.03E−02 4 8 LAB278_H00.82 4.54E−02 1 14 LAB278_H0 0.72 1.08E−01 1 15 LAB278_H0 0.77 7.19E−021 7 LAB278_H0 0.84 3.49E−02 1 1 LAB278_H0 0.78 6.69E−02 1 2 LAB278_H00.84 3.62E−02 1 13 LAB278_H0 0.77 7.58E−02 1 9 LAB278_H0 0.72 1.08E−01 110 LAB278_H0 0.82 4.60E−02 1 12 LAB278_H0 0.86 2.67E−02 1 4 LAB278_H00.93 7.94E−03 1 3 LNU74_H109 0.84 3.76E−02 2 7 LNU74_H109 0.79 6.24E−022 1 LNU74_H109 0.72 1.05E−01 2 2 LNU74_H109 0.87 2.44E−02 2 13LNU74_H109 0.81 4.97E−02 2 4 LNU74_H109 0.90 1.41E−02 2 3 LNU74_H1090.90 1.55E−02 1 8 LNU74_H109 0.70 1.20E−01 5 2 LNU74_H109 0.76 7.93E−025 10 LNU74_H109 0.73 1.01E−01 5 4 LYM350 0.71 1.15E−01 4 7 LYM350 0.758.38E−02 1 14 LYM350 0.77 7.58E−02 1 7 LYM350 0.85 3.25E−02 1 1 LYM3500.80 5.67E−02 1 2 LYM350 0.87 2.42E−02 1 13 LYM350 0.79 6.33E−02 1 9LYM350 0.82 4.64E−02 1 10 LYM350 0.84 3.60E−02 1 12 LYM350 0.86 2.74E−021 4 LYM350 0.95 3.31E−03 1 3 LYM350 0.73 9.73E−02 5 6 LYM490_H1 0.739.97E−02 5 10 LYM490_H1 0.71 1.08E−01 5 3 WYM104 0.70 1.18E−01 2 8WYM104 0.77 7.08E−02 1 8 WYM105 0.76 8.19E−02 5 10 WYM106 0.92 8.99E−032 13 WYM106 0.78 6.67E−02 2 4 WYM106 0.72 1.06E−01 2 3 WYM106 0.834.18E−02 1 14 WYM106 0.74 8.96E−02 1 15 WYM107 0.76 7.91E−02 4 13 WYM1070.74 9.30E−02 4 3 WYM107 0.86 2.87E−02 5 13 WYM107 0.74 9.56E−02 5 10WYM107 0.83 3.97E−02 5 3 WYM108 0.71 1.10E−01 2 14 WYM108 0.75 8.84E−022 15 WYM108 0.77 7.24E−02 2 1 WYM108 0.97 1.14E−03 2 13 WYM108 0.901.32E−02 2 4 WYM108 0.75 8.66E−02 2 5 WYM108 0.87 2.29E−02 2 3 WYM1080.96 2.85E−03 4 14 WYM108 0.71 1.13E−01 4 15 WYM108 0.74 8.94E−02 4 1WYM108 0.84 3.86E−02 4 13 WYM108 0.75 8.65E−02 4 12 WYM108 0.88 2.16E−024 4 WYM108 0.84 3.60E−02 1 11 WYM108 0.98 6.53E−04 1 8 WYM108 0.731.01E−02 5 14 WYM108 0.77 7.39E−02 5 13 WYM108 0.76 8.21E−01 5 4 WYM420.75 8.30E−02 4 15 WYM42 0.81 5.10E−02 4 2 WYM42 0.83 4.22E−02 4 9 WYM420.82 4.65E−02 4 10 WYM42 0.76 8.21E−02 4 12 WYM42 0.78 6.62E−02 4 5WYM42 0.74 9.51E−02 5 10 WYM42 0.80 5.77E−02 5 12 WYM43 0.79 6.26E−02 211 WYM43 0.89 1.79E−02 2 8 WYM44 0.75 8.72E−02 1 8 WYM44 0.74 9.07E−02 514 WYM46 0.72 1.08E−01 4 9 WYM46 0.80 5.41E−02 4 12 WYM46 0.80 5.47E−021 8 WYM47 0.74 8.96E−02 2 1 WYM47 0.81 5.09E−02 2 2 WYM47 0.86 2.73E−022 13 WYM47 0.74 9.51E−02 2 9 WYM47 0.86 2.99E−02 2 10 WYM47 0.882.01E−02 2 3 WYM47 0.94 6.10E−03 4 11 WYM47 0.79 6.34E−02 4 8 WYM47 0.928.73E−03 1 8 WYM47 0.78 6.55E−02 5 6 WYM48 0.89 1.72E−02 4 14 WYM48 0.796.00E−02 4 15 WYM48 0.83 4.27E−02 4 1 WYM48 0.76 8.23E−02 4 13 WYM480.73 9.69E−02 4 9 WYM48 0.73 1.01E−01 4 12 WYM48 0.88 2.02E−02 4 4 WYM480.73 1.01E−01 4 5 WYM48 0.71 1.14E−01 4 3 WYM48 0.70 1.19E−01 5 14 WYM480.73 1.01E−01 5 15 WYM48 0.80 5.64E−02 5 7 WYM48 0.73 1.03E−01 5 9 WYM510.73 1.01E−01 2 13 WYM51 0.76 7.92E−02 2 3 WYM51 0.80 5.80E−02 4 13WYM51 0.71 1.10E−01 1 8 WYM51 0.74 9.33E−02 5 14 WYM51 0.81 5.10E−02 5 1WYM51 0.85 3.02E−02 5 2 WYM51 0.81 4.98E−02 5 13 WYM51 0.70 1.19E−01 5 9WYM51 0.88 2.19E−02 5 10 WYM51 0.74 9.14E−02 5 12 WYM51 0.81 4.82E−02 54 WYM51 0.84 3.68E−02 5 3 WYM52 0.81 5.32E−02 1 15 WYM52 0.76 8.23E−02 11 WYM52 0.72 1.10E−01 1 4 WYM52 0.82 4.75E−02 1 5 WYM55 0.75 8.69E−02 214 WYM55 0.72 1.04E−01 2 13 WYM55 0.81 5.13E−02 2 4 WYM55 0.73 9.72E−024 1 WYM55 0.78 6.90E−02 4 13 WYM55 0.85 3.02E−02 4 4 WYM55 0.91 1.13E−025 14 WYM55 0.95 3.79E−03 5 15 WYM55 0.93 7.25E−03 5 1 WYM55 0.901.53E−02 5 2 WYM55 0.87 2.58E−02 5 13 WYM55 0.80 5.48E−02 5 9 WYM55 0.749.06E−02 5 10 WYM55 0.81 5.28E−02 5 12 WYM55 0.90 1.50E−02 5 4 WYM550.91 1.07E−02 5 5 WYM55 0.79 6.04E−02 5 3 WYM56 0.79 6.26E−02 1 8 WYM560.72 1.09E−01 5 7 WYM56 0.71 1.14E−01 5 9 WYM57 0.75 8.34E−02 2 8 WYM570.72 1.04E−01 4 11 WYM57 0.75 8.77E−02 4 6 WYM57 0.88 2.07E−02 1 8 WYM570.80 5.54E−02 5 8 WYM58 0.78 6.80E−02 4 15 WYM58 0.76 8.01E−02 4 1 WYM580.78 6.65E−02 4 4 WYM58 0.82 4.62E−02 4 5 WYM58 0.71 1.13E−01 1 9 WYM580.73 9.73E−02 1 10 WYM58 0.74 9.07E−02 1 12 WYM58 0.85 3.38E−02 5 8WYM59 0.84 3.64E−02 2 1 WYM59 0.78 6.84E−02 2 2 WYM59 0.95 3.51E−03 2 13WYM59 0.91 1.26E−02 2 4 WYM59 0.72 1.07E−01 2 5 WYM59 0.80 5.71E−02 2 3WYM60 0.72 1.08E−01 4 10 WYM60 0.94 4.67E−03 1 14 WYM60 0.96 2.41E−03 115 WYM60 0.84 3.65E−02 1 7 WYM60 0.99 2.79E−04 1 1 WYM60 0.98 9.07E−04 12 WYM60 0.77 7.26E−02 1 13 WYM60 0.92 9.66E−03 1 9 WYM60 0.82 4.37E−02 110 WYM60 0.87 2.40E−02 1 12 WYM60 0.92 8.62E−03 1 4 WYM60 0.93 7.16E−031 5 WYM60 0.93 7.76E−03 1 3 WYM61 0.97 1.27E−03 1 14 WYM61 0.84 3.79E−021 15 WYM61 0.79 5.91E−02 1 1 WYM61 0.82 4.69E−02 1 4 WYM61 0.75 8.30E−021 5 WYM61 0.96 2.90E−03 5 14 WYM61 0.85 3.04E−02 5 15 WYM61 0.711.10E−01 5 7 WYM61 0.91 1.11E−02 5 1 WYM61 0.83 4.06E−02 5 2 WYM61 0.805.41E−02 5 13 WYM61 0.77 7.23E−02 5 9 WYM61 0.82 4.58E−02 5 12 WYM610.93 6.82E−03 5 4 WYM61 0.77 7.24E−02 5 5 WYM61 0.88 2.19E−02 5 3 WYM620.71 1.13E−01 4 9 WYM62 0.91 1.15E−02 5 14 WYM62 0.84 3.73E−02 5 15WYM62 0.81 5.05E−02 5 7 WYM62 0.92 9.43E−03 5 1 WYM62 0.85 3.29E−02 5 2WYM62 0.83 3.86E−02 5 13 WYM62 0.83 3.87E−02 5 9 WYM62 0.76 8.20E−02 510 WYM62 0.87 2.29E−02 5 12 WYM62 0.93 7.66E−03 5 4 WYM62 0.76 8.00E−025 5 WYM62 0.93 6.96E−03 5 3 WYM63 0.73 9.91E−02 2 14 WYM63 0.81 4.94E−022 15 WYM63 0.80 5.62E−02 2 7 WYM63 0.87 2.40E−02 2 1 WYM63 0.93 6.48E−032 2 WYM63 0.97 9.98E−04 2 9 WYM63 0.98 8.42E−04 2 10 WYM63 0.98 7.24E−042 12 WYM63 0.77 7.59E−02 2 4 WYM63 0.77 7.34E−02 2 5 WYM63 0.93 7.59E−032 3 WYM63 0.71 1.14E−01 4 13 WYM63 0.72 1.04E−01 1 10 WYM64 0.739.94E−02 2 8 WYM65 0.86 2.69E−02 4 14 WYM65 0.79 6.15E−02 4 9 WYM65 0.891.77E−02 4 12 WYM65 0.95 3.57E−03 1 14 WYM65 0.80 5.45E−02 1 15 WYM650.85 1.37E−02 1 7 WYM65 0.79 5.88E−02 1 1 WYM65 0.72 1.05E−01 1 2 WYM650.78 6.67E−02 1 9 WYM65 0.81 5.33E−02 1 12 WYM65 0.81 5.30E−02 1 4 WYM650.71 1.12E−01 1 5 WYM65 0.78 6.69E−02 1 3 WYM65 0.90 1.39E−02 5 14 WYM650.97 1.40E−03 5 15 WYM65 0.81 4.25E−02 5 7 WYM65 0.99 1.29E−04 5 1 WYM650.99 2.82E−04 5 2 WYM65 0.84 3.52E−02 5 13 WYM65 0.94 5.10E−03 5 9 WYM650.89 1.75E−02 5 10 WYM65 0.91 1.21E−02 5 12 WYM65 0.94 5.74E−03 5 4WYM65 0.93 6.24E−03 5 5 WYM65 0.97 1.66E−03 5 3 WYM66 0.76 7.82E−02 4 12WYM66 0.89 1.73E−02 1 8 WYM67 0.76 8.19E−02 4 14 WYM67 0.92 9.94E−03 415 WYM67 0.94 6.11E−03 4 1 WYM67 0.89 1.87E−02 4 2 WYM67 0.79 6.29E−02 413 WYM67 0.92 8.36E−03 4 4 WYM67 0.94 5.61E−03 4 5 WYM67 0.76 7.92E−02 43 WYM67 0.72 1.08E−01 1 8 WYM67 0.70 1.20E−01 5 10 WYM69 0.86 2.68E−02 414 WYM69 0.71 1.16E−01 4 7 WYM69 0.72 1.08E−01 4 9 WYM69 0.75 8.28E−02 412 WYM69 0.93 7.43E−03 1 8 WYM69 0.81 5.30E−02 5 10 WYM98 0.77 7.43E−022 7 WYM98 0.76 8.12E−02 5 14 WYM98 0.86 2.98E−02 5 15 WYM98 0.853.25E−02 5 1 WYM98 0.82 4.46E−02 5 2 WYM98 0.78 6.57E−02 5 13 WYM98 0.777.61E−02 5 10 WYM98 0.78 6.88E−02 5 12 WYM98 0.90 1.51E−02 5 4 WYM980.89 1.85E−02 5 5 WYM98 0.77 7.11E−02 5 3 Correlations (R) between thegenes expression levels in various tissues and the phenotypicperformance. Corr. ID-correlation set ID according to the correlatedparameters Table 7 above. Exp. Set-Expression set. R = Pearsoncorrelation coefficient; P = p value.

Example 4 Production of Maize Transcriptome and High ThroughputCorrelation Analysis Using 60K Maize Oligonucleotide Micro-Array

To produce a high throughput correlation analysis, the present inventorsutilized a Maize oligonucleotide micro-array, produced by AgilentTechnologies [Hypertxt Transfer Protocol://World Wide Web (dot) chem.(dot) agilent (dot) com/Scripts/PDS (dot) asp?1Page=50879]. The arrayoligonucleotide represents about 60K Maize genes and transcriptsdesigned based on data from Public databases (Example 1). To definecorrelations between the levels of RNA expression and yield, biomasscomponents or vigor related parameters, various plant characteristics of12 different Maize hybrids were analyzed. Among them, 10 hybridsencompassing the observed variance were selected for RNA expressionanalysis. The correlation between the RNA levels and the characterizedparameters was analyzed using Pearson correlation test [HypertextTransfer Protocol://World Wide Web (dot) davidmlane (dot)com/hyperstat/A34739 (dot) html].

Experimental Procedures

12 Hybrid plants were grown in the field under normal growth conditions.Five tissues at different developmental stages including Ear (flowering-R1), leaf (flowering -R1). Leaf Grain from the basal ear part. Grainfrom the distal ear, representing different plant characteristics, weresampled and RNA was extracted as described in “GENERAL EXPERIMENTAL ANDBIOINFORMATICS METHODS”. For convenience, each micro-array expressioninformation tissue type has received a Set ID as summarized in Table 10below.

TABLE 10 Tissues used for Maize transcriptome expression sets ExpressionSet Set ID Ear normal Flowering-R1 1 Ear normal R2-R3 2 Internode normalV6 3 Internode normal Flowering-R1 4 Internode normal R2-R3 5 Leafnormal V6 6 Leaf normal Flowering-R1 7 Distal grain normal R3-R5 8 Table10: Provided are the identification (ID) letters of each of the Maizeexpression sets (1-8).

The following parameters were collected:

Grain Area (cm²)—

At the end of the growing period the grains were separated from the ear.A sample of ˜200 grains were weight, photographed and images wereprocessed using the below described image processing system. The grainarea was measured from those images and was divided by the number ofgrains.

Grain Length and Grain Width (cm)—

At the end of the growing period the grains were separated from the ear.A sample of ˜200 grains were weighted, photographed and images wereprocessed using the below described image processing system. The sum ofgrain lengths/or width (longest axis) was measured from those images andwas divided by the number of grains.

Ear Area (cm²)—

At the end of the growing period 6 ears were, photographed and imageswere processed using the below described image processing system. TheEar area was measured from those images and was divided by the number ofEars.

Ear Length and Ear Width (cm)—

At the end of the growing period 6 ears were, photographed and imageswere processed using the below described image processing system. TheEar length and width (longest axis) was measured from those images andwas divided by the number of ears.

The image processing system was used, which consists of a personaldesktop computer (Intel P4 3.0 GHz processor) and a public domainprogram—ImageJ 1.37. Java based image processing software, which wasdeveloped at the U.S. National Institutes of Health and is freelyavailable on the internet at Hypertext Transfer Protocol://rsbweb (dot)nih (dot) gov/. Images were captured in resolution of 10 Mega Pixels(3888×2592 pixels) and stored in a low compression JPEG (JointPhotographic Experts Group standard) format. Next, image processingoutput data for seed area and seed length was saved to text files andanalyzed using the JMP statistical analysis software (SAS institute).

Additional parameters were collected either by sampling 6 plants perplot or by measuring the parameter across all the plants within theplot.

Normalized Grain Weight Per Plant (Gr.)—

At the end of the experiment all ears from plots within blocks A-C werecollected. 6 ears were separately threshed and grains were weighted, alladditional ears were threshed together and weighted as well. The grainweight was normalized using the relative humidity to be 0%. Thenormalized average grain weight per ear was calculated by dividing thetotal normalized grain weight by the total number of ears per plot(based on plot). In case of 6 ears, the total grains weight of 6 earswas divided by 6.

Ear FW (Gr.)—

At the end of the experiment (when ears were harvested) total and 6selected ears per plots within blocks A-C were collected separately. Theplants with (total and 6) were weighted (Gr.) separately and the averageear per plant was calculated for total (Ear FW per plot) and for 6 (EarFW per plant).

Plant Height and Ear Height—

Plants were characterized for height at harvesting. In each measure, 6plants were measured for their height using a measuring tape. Height wasmeasured from ground level to top of the plant below the tassel. Earheight was measured from the ground level to the place were the main earis located

Leaf Number Per Plant—

Plants were characterized for leaf number during growing period at 5time points. In each measure, plants were measured for their leaf numberby counting all the leaves of 3 selected plants per plot.

Growth Rate was calculated using regression coefficient of leaf numberchange a long time course.

SPAD—

Chlorophyll content was determined using a Minolta SPAD 502 chlorophyllmeter and measurement was performed 64 days post sowing. SPAD meterreadings were done on young fully developed leaf. Three measurements perleaf were taken per plot. Data were taken after 46 and 54 days aftersowing (DPS).

Dry Weight Per Plant—

At the end of the experiment when all vegetative material from plotswithin blocks A-C were collected, weighted and divided by the number ofplants.

Ear Diameter [cm]—

The diameter of the ear at the mid of the ear was measured using aruler.

Cob Diameter [cm]—

The diameter of the cob without grains was measured using a ruler.

Kernel Row Number Per Ear—

The number of rows in each ear was counted. The average of 6 ears perplot was calculated.

TABLE 11 Maize correlated parameters (vectors) Correlated parameter withCorrelation ID Cob Diameter mm 1 DW per Plant based on 6 gr. 2 Ear Areacm² 3 Ear FW per Plant based on 6 gr. 4 Ear Height cm 5 Ear Length cm 6Ear Width cm 7 Ears FW per plant based on all gr. 8 Filled per Whole Ear9 Grain Area cm² 10 Grain Length cm 11 Grain Width cm 12 Growth RateLeaf Num 13 Kernel Row Number per Ear 14 Leaf Number per Plant 15Normalized Grain Weight per Plant based on all gr. 16 Normalized GrainWeight per plant based on 6 gr. 17 Percent Filled Ear 18 Plant Heightper Plot cm 19 SPAD 46DPS TP2 20 SPAD 54DPS TP5 21 Table 11. Providedare the maize correlated parameters (vectors). “DW” = Dry Weight; “FW” =Fresh Weight; “gr.” = grams; “cm” = centimeter; “SPAD” = chlorophylllevels. “TP2” = time point 2; “TP5” = time point 5.

Experimental Results

Twelve maize accessions were grown, and characterized for parameters, asdescribed above. The average for each parameter was calculated using theJMP software, and values are summarized in Tables 12-13 below.Subsequent correlation between the various transcriptome sets for all orsub set of lines was done by the bioinformatics unit and results wereintegrated into the database.

TABLE 12 Measured parameters in Maize Hybrid Ecotype/ Treatment Line-1Line-2 Line-3 Line-4 Line-5 Line-6 Line-7 Line-8 1 28.96 23.78 28.0525.73 28.72 25.78 26.43 25.19 2 657.50 472.02 641.11 580.56 655.56569.44 511.11 544.44 3 85.06 77.91 90.51 95.95 91.62 72.41 74.03 76.53 4245.83 189.88 262.22 263.89 272.22 177.78 188.89 197.22 5 135.17 116.31131.97 114.00 135.28 94.28 120.94 107.72 6 19.69 19.05 20.52 21.34 20.9218.23 19.02 18.57 7 5.58 5.10 5.67 5.53 5.73 5.23 5.22 5.33 8 278.19190.30 288.28 247.88 280.11 175.84 192.47 204.70 9 0.92 0.95 0.93 0.920.91 0.95 0.87 0.94 10 0.75 0.67 0.75 0.77 0.81 0.71 0.71 0.75 11 1.171.07 1.18 1.20 1.23 1.12 1.14 1.13 12 0.81 0.79 0.80 0.80 0.82 0.80 0.790.84 13 0.28 0.22 0.28 0.27 0.31 0.24 0.24 0.27 14 16.17 15.02 16.2015.89 16.17 15.17 16.00 14.83 15 12.00 8.40 11.69 11.78 11.94 12.3312.44 12.22 16 153.90 120.96 152.50 159.16 140.46 117.14 123.24 131.2717 140.68 128.93 153.67 176.98 156.61 119.67 119.69 133.51 18 80.6294.34 82.14 92.71 80.38 82.76 73.25 81.06 19 278.08 269.79 275.13 238.50286.94 224.83 264.44 251.61 21 54.28 57.18 56.01 59.68 54.77 59.14 57.9960.36 20 51.67 56.41 53.55 55.21 55.30 59.35 58.48 55.88 Provided arethe measured parameters under normal growth conditions of maizeaccessions according to the Correlation (Corr.) ID numbers (described inTable 16 above).

TABLE 13 Measured parameters in Maize Hybrid additional parametersEcotype/ Treatment Line-9 Line-10 Line-11 Line-12 1 26.67 2 574.17522.22 3 55.70 95.36 4 141.11 261.11 5 60.44 112.50 6 16.69 21.70 7 4.125.58 8 142.72 264.24 9 0.80 0.96 10 0.50 0.76 11 0.92 1.18 12 0.67 0.8113 0.19 0.30 14 14.27 15.39 15 9.28 12.56 16 40.84 170.66 17 54.32173.23 18 81.06 91.60 19 163.78 278.44 21 54.77 51.39 61.14 53.34 2052.98 53.86 59.75 49.99 Table 13. Provided are the measured parametersunder normal growth conditions of maize accessions according to theCorrelation (Corr.) ID numbers (described in Table 16 above).

TABLE 14 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance of maintenance of performance under drought conditionsacross maize lines Corr. Corr. Exp. Set Exp. Set Gene Name R P value setID Gene Name R P value set ID LAB278_H0 0.79 6.01E−02 2 9 LAB278_H0 0.777.11E−02 2 18 LNU74_H109 0.74 5.73E−02 1 16 LNU74_H109 0.81 2.65E−02 115 LNU74_H109 0.82 2.31E−02 1 13 LNU74_H109 0.73 6.23E−02 1 11LNU74_H109 0.71 7.22E−02 1 9 LNU74_H109 0.73 6.08E−02 1 10 LNU74_H1090.72 6.53E−02 1 7 LNU74_H109 0.76 1.86E−02 3 15 LNU74_H109 0.78 6.95E−022 6 LNU74_H109 0.73 9.68E−02 2 18 LYM350 0.75 3.19E−02 5 15 LYM350 0.865.88E−03 5 11 LYM350 0.81 1.50E−02 5 10 LYM350 0.78 3.76E−02 7 2 LYM3500.81 1.58E−02 8 1 LYM350 0.77 2.58E−02 8 13 LYM350 0.85 7.38E−03 8 2LYM350 0.71 4.75E−02 8 5 LYM350 0.81 1.46E−02 8 7 LYM350 0.82 1.19E−02 88 LYM350 0.75 3.39E−02 8 4 LYM350 0.80 5.47E−02 2 9 LYM350 0.86 2.75E−022 12 LYM490_H1 0.72 6.99E−02 4 15 LYM490_H1 0.97 2.52E−04 7 3 LYM490_H10.99 3.12E−05 7 16 LYM490_H1 0.81 2.83E−02 7 14 LYM490_H1 0.86 1.26E−027 13 LYM490_H1 0.81 2.65E−02 7 21 LYM490_H1 0.94 1.56E−03 7 11 LYM490_H10.94 1.57E−03 7 6 LYM490_H1 0.83 2.21E−02 7 9 LYM490_H1 0.92 3.00E−03 710 LYM490_H1 0.84 1.72E−02 7 18 LYM490_H1 0.87 1.13E−02 7 19 LYM490_H10.87 1.14E−02 7 5 LYM490_H1 0.95 1.25E−03 7 7 LYM490_H1 0.83 1.97E−02 78 LYM490_H1 0.83 2.13E−02 7 12 LYM490_H1 0.90 5.79E−03 7 4 LYM490_H10.99 9.71E−06 7 17 WYM104 0.76 2.85E−02 5 9 WYM104 0.70 1.21E−01 4 7WYM104 0.83 2.21E−02 4 14 WYM104 0.84 1.72E−02 7 3 WYM104 0.74 5.98E−027 16 WYM104 0.77 4.37E−02 7 14 WYM104 0.87 1.16E−02 7 6 WYM104 0.822.27E−02 7 18 WYM104 0.79 3.32E−02 7 4 WYM104 0.79 3.32E−02 7 17 WYM1040.75 1.90E−02 3 15 WYM104 0.74 2.34E−02 3 11 WYM104 0.74 2.19E−02 3 10WYM104 0.73 2.47E−02 3 7 WYM104 0.71 3.15E−02 3 12 WYM105 0.70 5.09E−025 18 WYM105 0.74 5.54E−02 4 14 WYM105 0.74 5.90E−02 4 5 WYM105 0.814.82E−02 7 1 WYM105 0.86 1.28E−02 1 9 WYM105 0.86 1.31E−02 1 19 WYM1050.81 2.65E−02 1 5 WYM105 0.71 7.62E−02 1 12 WYM105 0.74 3.68E−02 8 15WYM105 0.85 3.10E−02 2 3 WYM105 0.88 1.97E−02 2 16 WYM105 0.85 3.38E−022 13 WYM105 0.80 5.53E−02 2 11 WYM105 0.82 4.66E−02 2 6 WYM105 0.758.50E−02 2 18 WYM105 0.78 6.78E−02 2 7 WYM105 0.76 7.98E−02 2 8 WYM1050.82 4.37E−02 2 4 WYM105 0.81 4.85E−02 2 17 WYM106 0.83 1.12E−02 8 1WYM106 0.75 3.16E−02 8 13 WYM106 0.81 1.41E−02 8 2 WYM107 0.77 7.33E−024 1 WYM107 0.80 3.13E−02 4 2 WYM107 0.72 6.78E−02 1 12 WYM107 0.786.76E−02 2 14 WYM107 0.76 7.67E−02 2 2 WYM108 0.71 4.92E−02 5 10 WYM1080.88 2.08E−02 4 1 WYM108 0.87 1.12E−02 4 3 WYM108 0.81 2.62E−02 4 16WYM108 0.98 1.20E−04 4 14 WYM108 0.76 4.77E−02 4 13 WYM108 0.88 9.41E−034 11 WYM108 0.83 2.07E−02 4 6 WYM108 0.78 4.00E−02 4 10 WYM108 0.755.26E−02 4 5 WYM108 0.84 1.72E−02 4 7 WYM108 0.87 1.11E−02 4 8 WYM1080.90 5.64E−03 4 4 WYM108 0.83 1.97E−02 4 17 WYM108 0.76 4.64E−02 7 3WYM108 0.77 4.13E−02 7 16 WYM108 0.76 4.79E−02 7 6 WYM108 0.77 4.08E−027 9 WYM108 0.88 8.87E−03 7 18 WYM108 0.87 1.08E−02 7 19 WYM108 0.774.20E−02 7 5 WYM108 0.78 4.00E−02 7 17 WYM108 0.79 3.51E−02 1 9 WYM1080.77 4.11E−02 1 19 WYM108 0.92 1.06E−03 8 3 WYM108 0.82 1.35E−02 8 16WYM108 0.71 4.90E−02 8 14 WYM108 0.78 2.29E−02 8 13 WYM108 0.82 1.17E−028 11 WYM108 0.89 3.31E−03 8 6 WYM108 0.74 3.54E−02 8 10 WYM108 0.821.19E−02 8 2 WYM108 0.92 1.30E−03 8 7 WYM108 0.90 2.59E−03 8 8 WYM1080.95 2.85E−04 8 4 WYM108 0.85 7.71E−03 8 17 WYM108 0.72 1.93E−02 6 19WYM108 0.84 4.53E−03 3 15 WYM108 0.79 1.07E−02 3 11 WYM108 0.79 1.07E−023 10 WYM108 0.72 2.86E−02 3 7 WYM108 0.75 1.91E−02 3 12 WYM108 0.739.70E−02 2 3 WYM108 0.77 7.48E−02 2 6 WYM108 0.71 1.15E−01 2 10 WYM1080.82 4.75E−02 2 17 WYM42 0.71 7.65E−02 4 14 WYM42 0.70 7.93E−02 7 19WYM42 0.88 9.54E−03 1 3 WYM42 0.85 1.60E−02 1 16 WYM42 0.73 6.10E−02 114 WYM42 0.72 6.79E−02 1 11 WYM42 0.89 7.62E−03 1 6 WYM42 0.71 7.23E−021 9 WYM42 0.76 4.76E−02 1 18 WYM42 0.87 1.07E−02 1 19 WYM42 0.832.12E−02 1 5 WYM42 0.78 3.92E−02 1 7 WYM42 0.79 3.41E−02 1 8 WYM42 0.822.48E−02 1 4 WYM42 0.85 1.65E−02 1 17 WYM42 0.78 1.29E−02 6 1 WYM42 0.721.10E−01 2 12 WYM43 0.82 2.32E−02 1 3 WYM43 0.80 3.01E−02 1 16 WYM430.80 3.06E−02 1 11 WYM43 0.77 4.38E−02 1 6 WYM43 0.79 3.34E−02 1 10WYM43 0.70 7.78E−02 1 19 WYM43 0.80 3.09E−02 1 5 WYM43 0.76 4.81E−02 1 7WYM43 0.71 7.66E−02 1 8 WYM43 0.73 6.11E−02 1 12 WYM43 0.79 3.51E−02 1 4WYM43 0.85 1.54E−02 1 17 WYM44 0.80 1.65E−02 5 3 WYM44 0.75 3.10E−02 516 WYM44 0.73 4.01E−02 5 11 WYM44 0.85 8.13E−03 5 6 WYM44 0.75 3.14E−025 7 WYM44 0.71 4.64E−02 5 8 WYM44 0.80 1.77E−02 5 4 WYM44 0.76 3.01E−025 17 WYM44 0.71 1.15E−01 4 1 WYM44 0.70 1.18E−01 7 1 WYM44 0.72 6.99E−021 2 WYM44 0.86 2.73E−02 2 3 WYM44 0.73 9.73E−02 2 16 WYM44 0.70 1.21E−012 13 WYM44 0.87 2.46E−02 2 11 WYM44 0.84 3.44E−02 2 6 WYM44 0.824.48E−02 2 7 WYM44 0.79 6.07E−02 2 8 WYM44 0.85 3.19E−02 2 4 WYM44 0.853.29E−02 2 17 WYM46 0.72 6.62E−02 4 14 WYM46 0.79 3.46E−02 4 13 WYM460.70 7.79E−02 4 2 WYM46 0.79 3.33E−02 1 3 WYM46 0.75 5.45E−02 1 16 WYM460.90 5.88E−03 1 14 WYM46 0.71 7.63E−02 1 11 WYM46 0.82 2.40E−02 1 6WYM46 0.75 5.23E−02 1 19 WYM46 0.90 5.71E−03 1 5 WYM46 0.76 4.53E−02 1 7WYM46 0.91 4.99E−03 1 8 WYM46 0.88 8.45E−03 1 4 WYM46 0.76 4.71E−02 1 17WYM46 0.70 5.11E−02 8 5 WYM46 0.74 9.12E−02 2 12 WYM47 0.74 5.93E−02 4 3WYM47 0.84 1.75E−02 4 16 WYM47 0.78 3.66E−02 4 13 WYM47 0.80 3.15E−02 411 WYM47 0.84 1.86E−02 4 9 WYM47 0.86 1.38E−02 4 10 WYM47 0.95 1.12E−034 19 WYM47 0.93 2.40E−03 4 5 WYM47 0.90 6.28E−03 4 7 WYM47 0.78 3.75E−024 8 WYM47 0.86 1.28E−02 4 12 WYM47 0.70 7.98E−02 4 4 WYM47 0.77 4.41E−024 17 WYM47 0.75 5.46E−02 7 3 WYM47 0.82 2.37E−02 7 16 WYM47 0.793.26E−02 7 13 WYM47 0.73 6.09E−02 7 6 WYM47 0.79 3.63E−02 7 9 WYM47 0.745.81E−02 7 10 WYM47 0.94 1.47E−03 7 19 WYM47 0.80 3.10E−02 7 5 WYM470.79 3.63E−02 7 7 WYM47 0.75 5.04E−02 7 8 WYM47 0.73 6.24E−02 7 12 WYM470.75 5.11E−02 7 17 WYM47 0.78 4.00E−02 1 16 WYM47 0.78 3.93E−02 1 13WYM47 0.74 5.93E−02 1 11 WYM47 0.82 2.49E−02 1 9 WYM47 0.83 2.12E−02 110 WYM47 0.89 6.74E−03 1 19 WYM47 0.83 2.17E−02 1 5 WYM47 0.83 2.05E−021 7 WYM47 0.88 9.38E−03 1 12 WYM47 0.86 5.97E−03 8 1 WYM47 0.79 1.92E−028 13 WYM47 0.81 1.58E−02 8 2 WYM47 0.72 1.90E−02 6 3 WYM47 0.80 5.44E−036 16 WYM47 0.71 2.19E−02 6 13 WYM47 0.70 2.32E−02 6 6 WYM47 0.721.78E−02 6 9 WYM47 0.73 1.73E−02 6 10 WYM47 0.85 1.72E−03 6 19 WYM470.71 2.07E−02 6 5 WYM47 0.77 9.12E−03 6 7 WYM47 0.74 1.52E−02 6 12 WYM470.74 1.38E−02 6 17 WYM47 0.77 1.52E−02 3 3 WYM47 0.82 6.40E−03 3 16WYM47 0.74 2.31E−02 3 13 WYM47 0.88 1.88E−03 3 11 WYM47 0.72 2.77E−02 36 WYM47 0.76 1.78E−02 3 9 WYM47 0.92 4.39E−04 3 10 WYM47 0.85 4.01E−03 319 WYM47 0.75 2.00E−02 3 5 WYM47 0.86 2.75E−03 3 7 WMY47 0.94 1.94E−04 312 WYM47 0.87 2.48E−03 3 17 WYM47 0.70 1.21E−01 2 3 WYM47 0.72 1.10E−012 14 WYM47 0.80 5.45E−02 2 11 WYM47 0.75 8.63E−02 2 6 WYM47 0.749.41E−02 2 19 WYM47 0.73 1.00E−01 2 4 WYM48 0.80 1.68E−02 5 9 WYM48 0.764.67E−02 7 9 WYM48 0.86 1.40E−02 1 9 WYM48 0.81 2.58E−02 1 12 WYM48 0.721.09E−01 2 12 WYM51 0.82 2.43E−02 4 3 WYM51 0.78 3.85E−02 4 14 WYM510.70 7.79E−02 4 11 WYM51 0.84 1.71E−02 4 6 WYM51 0.75 5.10E−02 4 8 WYM510.86 1.25E−02 4 4 WYM51 0.75 4.98E−02 4 17 WYM51 0.78 3.71E−02 1 16WYM51 0.74 5.74E−02 1 11 WYM51 0.98 1.75E−04 1 9 WYM51 0.82 2.28E−02 110 WYM51 0.89 6.88E−03 1 19 WYM51 0.80 3.01E−02 1 5 WYM51 0.83 2.10E−021 7 WYM51 0.90 6.23E−03 1 12 WYM51 0.70 7.79E−02 1 17 WYM51 0.872.50E−02 2 3 WYM51 0.76 8.24E−02 2 16 WYM51 0.84 3.58E−02 2 11 WYM510.91 1.07E−02 2 6 WYM51 0.72 1.05E−01 2 7 WYM51 0.80 5.39E−02 2 4 WYM510.83 4.06E−02 2 17 WYM52 0.81 1.43E−02 8 1 WYM52 0.77 2.66E−02 8 3 WYM520.90 2.20E−03 8 16 WYM52 0.88 3.75E−03 8 13 WYM52 0.77 2.48E−02 8 11WYM52 0.79 2.00E−02 8 10 WYM52 0.89 3.02E−03 8 2 WYM52 0.72 4.46E−02 8 5WYM52 0.94 6.36E−04 8 7 WYM52 0.95 2.33E−04 8 8 WYM52 0.88 4.32E−03 8 4WYM55 0.83 1.17E−02 5 12 WYM55 0.85 3.37E−02 4 1 WYM55 0.85 1.45E−02 4 2WYM55 0.75 5.09E−02 7 2 WYM55 0.86 2.98E−02 1 1 WYM55 0.70 7.71E−02 1 14WYM55 0.71 7.59E−02 1 15 WYM55 0.72 6.65E−02 1 2 WYM55 0.87 5.35E−03 8 1WYM55 0.75 3.13E−02 8 14 WYM55 0.85 8.04E−03 8 13 WYM55 0.77 2.68E−02 811 WYM55 0.76 2.91E−02 8 10 WYM55 0.97 5.99E−05 8 2 WYM55 0.79 1.87E−028 5 WYM55 0.90 2.46E−03 8 7 WYM55 0.86 5.97E−03 8 8 WYM55 0.81 1.55E−028 4 WYM55 0.72 2.97E−02 3 15 WYM56 0.73 9.99E−02 4 1 WYM56 0.79 3.59E−024 3 WYM56 0.76 4.89E−02 4 16 WYM56 0.87 1.15E−02 4 14 WYM56 0.726.82E−02 4 15 WYM56 0.74 5.58E−02 4 13 WYM56 0.88 9.81E−03 4 11 WYM560.73 6.16E−02 4 6 WYM56 0.79 3.63E−02 4 10 WYM56 0.80 3.26E−02 4 7 WYM560.75 5.30E−02 4 8 WYM56 0.81 2.64E−02 4 4 WYM56 0.79 3.53E−02 4 17 WYM560.79 3.57E−02 7 19 WYM56 0.72 1.84E−02 6 19 WYM56 0.71 2.14E−02 6 5WYM56 0.80 5.41E−02 7 3 WYM56 0.73 9.81E−02 2 16 WYM56 0.72 1.09E−01 213 WYM56 0.84 3.42E−02 2 6 WYM56 0.89 1.65E−02 2 18 WYM56 0.88 2.21E−022 17 WYM57 0.77 2.55E−02 5 13 WYM57 0.81 4.08E−03 6 20 WYM57 0.796.14E−02 2 3 WYM57 0.79 6.07E−02 2 16 WYM57 0.82 4.61E−02 2 13 WYM570.80 5.34E−02 2 6 WYM57 0.93 6.49E−03 2 18 WYM57 0.90 1.47E−02 2 17WYM58 0.76 2.88E−02 5 15 WYM58 0.86 5.85E−03 5 12 WYM58 0.70 7.99E−02 79 WYM58 0.75 5.00E−02 7 19 WYM58 0.93 7.01E−03 1 1 WYM58 0.71 2.27E−02 618 WYM58 0.79 6.31E−02 2 9 WYM58 0.70 1.18E−01 2 18 WYM58 0.87 2.59E−022 12 WYM59 0.81 1.52E−02 5 1 WYM59 0.75 3.04E−02 5 2 WYM60 0.95 1.22E−034 3 WYM60 0.95 1.13E−03 4 16 WYM60 0.82 2.29E−02 4 14 WYM60 0.851.50E−02 4 13 WYM60 0.89 8.05E−03 4 11 WYM60 0.91 4.97E−03 4 6 WYM600.72 6.73E−02 4 9 WYM60 0.88 8.90E−03 4 10 WYM60 0.92 3.77E−03 4 19WYM60 0.95 9.43E−04 4 5 WYM60 0.93 2.75E−03 4 7 WYM60 0.92 3.01E−03 4 8WYM60 0.79 3.65E−02 4 12 WYM60 0.92 3.07E−03 4 4 WYM60 0.94 1.61E−03 417 WYM60 0.71 7.22E−02 7 9 WYM60 0.71 7.67E−02 1 10 WYM60 0.73 6.07E−021 12 WYM61 0.79 3.33E−02 4 3 WYM61 0.90 6.35E−03 4 16 WYM61 0.736.34E−02 4 13 WYM61 0.90 6.38E−03 4 11 WYM61 0.71 7.45E−02 4 6 WYM610.91 4.50E−03 4 9 WYM61 0.94 1.48E−03 4 10 WYM61 0.80 3.21E−02 4 19WYM61 0.80 3.09E−02 4 5 WYM61 0.89 6.54E−03 4 7 WYM61 0.96 7.57E−04 4 12WYM61 0.89 7.56E−03 4 17 WYM61 0.70 7.75E−02 7 3 WYM61 0.70 7.91E−02 7 6WYM61 0.73 6.01E−02 7 18 WYM61 0.70 7.80E−02 1 9 WYM61 0.80 3.01E−02 112 WYM61 0.80 1.61E−02 8 19 WYM61 0.85 7.85E−03 8 5 WYM61 0.73 2.63E−023 12 WYM62 0.81 1.48E−02 8 3 WYM62 0.86 6.19E−03 8 16 WYM62 0.782.24E−02 8 6 WYM62 0.78 2.20E−02 8 4 WYM62 0.80 1.82E−02 8 17 WYM63 0.793.62E−02 7 21 WYM63 0.73 6.12E−02 7 9 WYM63 0.78 3.98E−02 7 10 WYM630.75 5.34E−02 7 19 WYM63 0.70 7.92E−02 7 7 WYM63 0.87 1.04E−02 7 12WYM63 0.71 7.36E−02 1 16 WYM63 0.72 6.58E−02 1 9 WYM63 0.93 2.32E−03 119 WYM63 0.92 3.36E−03 1 5 WYM63 0.76 4.79E−02 1 7 WYM63 0.72 6.85E−02 18 WYM63 0.72 6.77E−02 1 1.2 WYM63 0.92 3.66E−04 3 3 WYM63 0.91 6.53E−043 16 WYM63 0.94 2.01E−04 3 13 WYM63 0.87 2.57E−03 3 11 WYM63 0.853.74E−03 3 6 WYM63 0.73 2.69E−02 3 9 WYM63 0.88 1.54E−03 3 10 WYM63 0.809.36E−03 3 19 WYM63 0.75 2.09E−02 3 5 WYM63 0.91 6.58E−04 3 7 WYM63 0.891.51E−03 3 8 WYM63 0.82 6.92E−03 3 12 WYM63 0.90 8.54E−04 3 4 WYM63 0.923.57E−04 3 17 WYM63 0.83 4.19E−02 2 2 WYM64 0.85 3.25E−02 4 1 WYM64 0.805.63E−02 2 9 WYM64 0.72 1.05E−01 2 18 WYM65 0.72 6.93E−02 4 18 WYM660.78 3.72E−02 4 19 WYM66 0.75 5.05E−02 4 5 WYM66 0.73 6.35E−02 1 5 WYM670.90 2.40E−03 5 11 WYM67 0.80 1.66E−02 5 10 WYM67 0.75 8.67E−02 4 1WYM67 0.89 7.62E−03 4 2 WYM67 0.73 9.89E−02 7 1 WYM67 0.87 2.40E−02 1 1WYM67 0.80 2.92E−02 1 2 WYM67 0.75 3.23E−02 8 16 WYM67 0.82 4.36E−02 2 3WYM67 0.73 9.92E−02 2 11 WYM67 0.78 6.51E−02 2 6 WYM67 0.72 1.08E−01 218 WYM67 0.73 9.64E−02 2 7 WYM67 0.76 8.23E−02 2 4 WYM67 0.84 3.77E−02 217 WYM69 0.71 4.86E−02 5 6 WYM69 0.72 6.59E−02 4 3 WYM69 0.79 3.50E−02 416 WYM69 0.71 7.33E−02 4 6 WYM69 0.86 1.37E−02 4 9 WYM69 0.93 2.72E−03 419 WYM69 0.81 2.77E−02 4 5 WYM69 0.75 5.03E−02 4 7 WYM69 0.74 5.86E−02 417 WYM69 0.91 1.12E−02 7 1 WYM69 0.87 9.95E−03 7 3 WYM69 0.87 1.09E−02 716 WYM69 0.92 3.64E−03 7 14 WYM69 0.79 3.38E−02 7 15 WYM69 0.84 1.73E−027 13 WYM69 0.84 1.69E−02 7 11 WYM69 0.86 1.33E−02 7 6 WYM69 0.745.91E−02 7 9 WYM69 0.84 1.80E−02 7 10 WYM69 0.80 3.03E−02 7 19 WYM690.85 1.63E−02 7 5 WYM69 0.89 8.01E−03 7 7 WYM69 0.89 7.70E−03 7 8 WYM690.77 4.41E−02 7 12 WYM69 0.87 1.05E−02 7 4 WYM69 0.84 1.73E−02 7 17WYM69 0.72 6.91E−02 1 11 WYM69 0.81 2.57E−02 1 9 WYM69 0.78 3.77E−02 110 WYM69 0.76 4.90E−02 1 7 WYM69 0.87 9.98E−03 1 12 WYM69 0.72 1.89E−026 16 WYM69 0.74 2.28E−02 3 15 WYM69 0.76 1.78E−02 3 13 WYM69 0.817.98E−03 3 11 WYM69 0.85 3.77E−03 3 10 WYM69 0.76 1.84E−02 3 7 WYM690.83 5.48E−03 3 12 WYM69 0.92 9.31E−03 2 3 WYM69 0.96 1.84E−03 2 16WYM69 0.96 1.89E−03 2 13 WYM69 0.92 8.68E−03 2 11 WYM69 0.98 4.20E−04 26 WYM69 0.90 1.52E−02 2 10 WYM69 0.87 2.60E−02 2 18 WYM69 0.83 4.32E−022 19 WYM69 0.95 4.23E−03 2 7 WYM69 0.95 3.79E−03 2 8 WYM69 0.96 2.84E−032 4 WYM69 0.91 1.23E−02 2 17 WYM98 0.86 5.98E−03 5 11 WYM98 0.772.44E−02 5 10 WYM98 0.71 5.07E−02 5 2 WYM98 0.73 3.98E−02 5 7 WYM98 0.815.31E−02 4 1 WYM98 0.82 2.26E−02 4 2 WYM98 0.78 6.79E−02 7 1 WYM98 0.862.77E−02 1 1 WYM98 0.73 6.50E−02 1 16 WYM98 0.73 6.32E−02 1 15 WYM980.71 7.44E−02 1 13 WYM98 0.82 2.25E−02 1 11 WYM98 0.87 1.02E−02 1 10WYM98 0.84 1.76E−02 1 2 WYM98 0.79 3.55E−02 1 7 WYM98 0.87 1.02E−02 1 12WYM98 0.71 7.46E−02 1 17 WYM98 0.74 3.45E−02 8 1 WYM98 0.74 3.49E−02 8 3WYM98 0.75 3.15E−02 8 8 WYM98 0.73 4.09E−02 8 4 WYM98 0.70 5.22E−02 8 17WYM98 0.73 2.53E−02 3 15 WYM98 0.71 1.12E−01 2 10 WYM98 0.82 4.54E−02 22 Correlations (R) between the genes expression levels in varioustissues and the phenotypic performance. Corr. ID-correlation set IDaccording to the correlated parameters Table 11 above. Exp.Set-Expression set. R = Pearson correlation coefficient; P = p value.

Example 5 Production of Barley Transcriptome and High ThroughputCorrelation Analysis Using 44K Barley Oligonucleotide Micro-Array

In order to produce a high throughput correlation analysis comparingbetween plant phenotype and gene expression level, the present inventorsutilized a Barley oligonucleotide micro-array, produced by AgilentTechnologies [Hypertext Transfer Protocol://World Wide Web (dot) chem.(dot) agilent (dot) com/Scripts/PDS (dot) asp?1Page=50879]. The arrayoligonucleotide represents about 47.500 Barley genes and transcripts. Inorder to define correlations between the levels of RNA expression andyield or vigor related parameters, various plant characteristics of 25different Barley accessions were analyzed in the field under normalgrowth conditions. Among them, 13 accessions encompassing the observedvariance were selected for RNA expression analysis. The correlationbetween the RNA levels and the characterized parameters was analyzedusing Pearson correlation test [Hypertext Transfer Protocol://World WideWeb (dot) davidmlane (dot) com/hyperstat/A34739 (dot) html].

Experimental Procedures

Analyzed Barley Tissues—

Five tissues at different developmental stages [meristem, flower,booting spike, stem, flag leaf], representing different plantcharacteristics, were sampled and RNA was extracted as described above.Each micro-array expression information tissue type has received a SetID as summarized in Table 15 below.

TABLE 15 Barley transcriptome expression sets Expression Set Set IDYield barley booting spike 1 Yield barley flower 2 Yield barley meristem3 Yield barley stem 4 Table 15: Provided are the barley transcriptomeexpression sets.

Barley Yield Components and Vigor Related Parameters Assessment—

25 Barley accessions in 4 repetitive blocks (named A, B, C, and D), eachcontaining 4 plants per plot were grown at net house. Plants werephenotyped on a daily basis following the standard descriptor of barley(Table 16, below). Harvest was conducted while 50% of the spikes weredry to avoid spontaneous release of the seeds. Plants were separated tothe vegetative part and spikes, of them, 5 spikes were threshed (grainswere separated from the glumes) for additional grain analysis such assize measurement, grain count per spike and grain yield per spike. Allmaterial was oven dried and the seeds were threshed manually from thespikes prior to measurement of the seed characteristics (weight andsize) using scanning and image analysis. The image analysis systemincluded a personal desktop computer (Intel P4 3.0 GHz processor) and apublic domain program—ImageJ 1.37 (Java based image processing program,which was developed at the U.S. National Institutes of Health and freelyavailable on the internet [Hypertext Transfer Protocol://rsbweb (dot)nih (dot) gov/]. Next, analyzed data was saved to text files andprocessed using the JMP statistical analysis software (SAS institute).

TABLE 16 Barley standard descriptors Trait Parameter Range DescriptionGrowth habit Scoring 1-9 Prostrate (1) or Erect (9) Hairiness of ScoringP (Presence)/ Absence (1) or basal leaves A (Absence) Presence (2) StemScoring Green (1), Basal only pigmentation or Half or more (5) Days toDays Days from sowing to Flowering emergence on awns Plant heightCentimeter Height from ground level (cm) to top of the longest spikeexcluding awns Spikes per Number Terminal Counting plant Spike lengthCentimeter Terminal Counting (cm) 5 spikes per plant Grains per NumberTerminal Counting spike 5 spikes per plant Vegetative dry GramOven-dried for weight 48 hours at 70° C. Spikes dry Gram Oven-dried forweight 48 hours at 30° C. Table 16. Barley standard descriptors.

Grains Per Spike—

At the end of the experiment (50% of the spikes were dry) all spikesfrom plots within blocks A-D were collected. The total number of grainsfrom 5 spikes that were manually threshed was counted. The average grainper spike was calculated by dividing the total grain number by thenumber of spikes.

Grain Average Size (cm)—

At the end of the experiment (50% of the spikes were dry) all spikesfrom plots within blocks A-D were collected. The total grains from 5spikes that were manually threshed were scanned and images were analyzedusing the digital imaging system. Grain scanning was done using Brotherscanner (model DCP-135), at the 200 dpi resolution and analyzed withImage J software. The average grain size was calculated by dividing thetotal grain size by the total grain number.

Grain Average Weight (Mgr)—

At the end of the experiment (50% of the spikes were dry) all spikesfrom plots within blocks A-D were collected. The total grains from 5spikes that were manually threshed were counted and weight. The averageweight was calculated by dividing the total weight by the total grainnumber.

Grain Yield Per Spike (Gr)—

At the end of the experiment (50% of the spikes were dry) all spikesfrom plots within blocks A-D were collected. The total grains from 5spikes that were manually threshed were weight. The grain yield wascalculated by dividing the total weight by the spike number.

Spike Length Analysis—

At the end of the experiment (50% of the spikes were dry) all spikesfrom plots within blocks A-D were collected. The five chosen spikes perplant were measured using measuring tape excluding the awns.

Spike Number Analysis—

At the end of the experiment (50% of the spikes were dry) all spikesfrom plots within blocks A-D were collected. The spikes per plant werecounted.

Growth Habit Scoring—

At the growth stage 10 (booting), each of the plants was scored for itsgrowth habit nature. The scale that was used was 1 for prostate naturetill 9 for erect.

Hairiness of Basal Leaves—

At the growth stage 5 (leaf sheath strongly erect; end of tillering),each of the plants was scored for its hairiness nature of the leafbefore the last. The scale that was used was 1 for prostate nature till9 for erect.

Plant Height—

At the harvest stage (50% of spikes were dry) each of the plants wasmeasured for its height using measuring tape. Height was measured fromground level to top of the longest spike excluding awns.

Days to Flowering—

Each of the plants was monitored for flowering date. Days of floweringwas calculated from sowing date till flowering date.

Stem Pigmentation—

At the growth stage 10 (booting), each of the plants was scored for itsstem color. The scale that was used was 1 for green till 5 for fullpurple.

Vegetative Dry Weight and Spike Yield—

At the end of the experiment (50% of the spikes were dry) all spikes andvegetative material from plots within blocks A-D were collected. Thebiomass and spikes weight of each plot was separated, measured anddivided by the number of plants.

Dry weight=total weight of the vegetative portion above ground(excluding roots) after drying at 70° C. in oven for 48 hours;

Spike yield per plant=total spike weight per plant (Gr) after drying at30° C. in oven for 48 hours.

Harvest Index (for Barley)—

The harvest index was calculated using Formula XI.Harvest Index=Average spike dry weight per plant/(Average vegetative dryweight per plant+Average spike dry weight per plant)  Formula XI

TABLE 17 Barley correlated parameters (vectors) Correlated parameterwith Correlation ID Grain weight 1 Grains Size 2 Grains per spike 3Growth habit 4 Hairiness of basal leaves 5 Plant height 6 Seed Yield of5 Spikes 7 Spike length 8 Spikes per plant 9 Stem pigmentation 10Vegetative dry weight 11 days to flowering 12 Table 17. Provided are theBarley correlated parameters.

Experimental Results

13 different Barley accessions were grown and characterized for 13parameters as described above. The average for each of the measuredparameter was calculated using the JMP software and values aresummarized in Tables 18 and 19 below. Subsequent correlation analysisbetween the various transcriptome sets (Table 15) and the averageparameters (Tables 18 and 19) was conducted. Follow, results wereintegrated to the database.

TABLE 18 Measured parameters of correlation IDs in Barley accessionsEcotype/ Treat- ment Line-1 Line-2 Line-3 Line-4 Line-5 Line-6 Line-7 135.05 28.06 28.76 17.87 41.22 29.73 34.99 2 0.27 0.23 0.24 0.17 0.290.28 0.28 3 20.23 17.98 17.27 17.73 14.47 16.78 14.07 4 2.60 2.00 1.923.17 4.33 2.69 3.50 5 1.53 1.33 1.69 1.08 1.42 1.69 1.19 6 134.27 130.50138.77 114.58 127.75 129.38 121.63 7 3.56 2.54 2.58 1.57 3.03 2.52 2.628 12.04 10.93 11.83 9.90 11.68 11.53 11.22 9 48.85 48.27 37.42 61.9233.27 41.69 40.63 10 1.13 2.50 1.69 1.75 2.33 2.31 2.19 11 78.87 66.1468.49 53.39 68.30 74.17 58.33 12 62.40 64.08 65.15 58.92 63.00 70.5460.88 Table 18. Provided are the values of each of the parametersmeasured in Barley accessions according to the correlationidentifications presented in Table 17.

TABLE 19 Barley accessions, additional measured parameters Ecotype/Treatment Line-8 Line-9 Line-10 Line-11 Line-12 Line-13 1 20.58 37.1325.22 27.50 29.56 19.58 2 0.19 0.27 0.22 0.22 0.27 0.18 3 21.54 13.4012.12 12.10 15.28 17.07 4 3.00 2.47 3.60 3.67 3.50 3.00 5 1.00 1.60 1.301.17 1.08 1.17 6 126.80 121.40 103.89 99.83 118.42 117.17 7 2.30 2.681.55 1.68 2.35 1.67 8 11.11 10.18 8.86 8.58 10.51 9.80 10 62.00 50.6040.00 49.33 43.09 51.40 11 2.30 3.07 1.70 1.83 1.58 2.17 12 62.23 68.3135.35 38.32 56.15 42.68 1 20.58 37.13 25.22 27.50 29.56 19.58 2 0.190.27 0.22 0.22 0.27 0.18 3 21.54 13.40 12.12 12.10 15.28 17.07 4 3.002.47 3.60 3.67 3.50 3.00 5 1.00 1.60 1.30 1.17 1.08 1.17 6 126.80 121.40103.89 99.83 118.42 117.17 7 2.30 2.68 1.55 1.68 2.35 1.67 8 11.11 10.188.86 8.58 10.51 9.80 9 62.00 50.60 40.00 49.33 43.09 51.40 10 2.30 3.071.70 1.83 1.58 2.17 11 62.23 68.31 35.35 38.32 56.15 42.68 12 58.1060.40 52.80 53.00 64.58 56.00 9 62.00 50.60 Table 19. Provided are thevalues of each of the parameters measured in Barley accessions accordingto the correlation identifications presented in Table 17.

TABLE 20 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tisses and the phenotypicperformance of maintenance of performance under drought conditionsacross barley varieties Gene P Exp. Corr. Gene P Exp. Corr. Name R valueset Set ID Name R value set Set ID LYM320 0.86 5.69E−03 1 9 LYM332 0.783.71E−02 2 9 LYM90 0.77 1.63E−02 1 2 LYM90 0.81 7.77E−03 1 1 LYM90 0.872.38E−03 1 7 LYM90 0.78 1.33E−02 1 11 WYM1 0.79 4.05E−03 1 4 WYM11 0.751.88E−02 3 2 WYM11 0.75 2.07E−02 3 1 WYM11 0.76 1.74E−02 3 7 WYM12 0.713.38E−02 1 6 WYM12 0.72 2.81E−02 1 12 WYM12 0.72 4.44E−02 2 2 WYM12 0.724.28E−02 2 1 WYM12 0.76 1.12E−02 2 5 WYM12 0.90 1.00E−03 3 2 WYM12 0.872.11E−03 3 1 WYM12 0.72 1.24E−02 3 6 WYM12 0.74 3.73E−02 3 9 WYM12 0.775.72E−03 3 7 WYM12 0.75 8.25E−03 3 11 WYM12 0.72 3.00E−02 3 12 WYM120.89 2.48E−04 3 5 WYM13 0.70 5.28E−02 2 1 WYM13 0.71 5.02E−02 2 6 WYM130.76 2.91E−02 2 8 WYM13 0.80 1.70E−02 2 7 WYM13 0.81 1.38E−02 2 11 WYM130.71 4.74E−02 2 12 WYM16 0.75 1.16E−02 2 9 WYM16 0.84 9.12E−03 2 3 WYM170.79 1.22E−02 3 7 WYM18 0.72 1.28E−02 1 12 WYM19 0.80 1.03E−02 1 2 WYM190.77 1.50E−02 1 1 WYM19 0.81 7.84E−03 1 5 WYM19 0.80 1.64E−02 2 4 WYM20.74 9.86E−03 3 6 WYM2 0.75 1.95E−02 3 8 WYM2 0.86 2.88E−03 3 7 WYM20.79 1.11E−02 3 11 WYM20 0.75 1.98E−02 3 2 WYM20 0.75 1.96E−02 3 7 WYM30.80 9.56E−03 1 2 WYM3 0.82 6.45E−03 1 1 WYM3 0.71 3.33E−02 1 7 WYM40.79 1.14E−02 1 2 WYM4 0.74 2.40E−02 1 1 WYM4 0.80 9.37E−03 1 7 WYM70.75 3.38E−02 2 10 WYM7 0.80 1.03E−02 3 3 WYM9 0.78 1.36E−02 3 2 WYM90.81 7.50E−03 3 1 WYM9 0.80 9.80E−03 3 7 Table 20. Correlations (R)between the genes expression levels in various tissues and thephenotypic performance. “Corr. ID” - correlation set ID according to thecorrelated parameters Table 17 above. “Exp. Set” - Expression set. “R” =Pearson correlation coefficient; “P” = p value.

Example 6 Production of Barley Transcriptome and High ThroughputCorrelation Analysis Using 60K Barley Oligonucleotide Micro-Array

In order to produce a high throughput correlation analysis comparingbetween plant phenotype and gene expression level, the present inventorsutilized a Barley oligonucleotide micro-array, produced by AgilentTechnologies [Hypertext Transfer Protocol://World Wide Web (dot) chem.(dot) agilent (dot) com/Scripts/PDS (dot) asp?1Page=50879]. The arrayoligonucleotide represents about 60K Barley genes and transcripts. Inorder to define correlations between the levels of RNA expression andyield or vigor related parameters, various plant characteristics of 15different Barley accessions were analyzed. Among them, 10 accessionsencompassing the observed variance were selected for RNA expressionanalysis. The correlation between the RNA levels and the characterizedparameters was analyzed using Pearson correlation test [HypertextTransfer Protocol://World Wide Web (dot) davidmlane (dot)com/hyperstat/A34739 (dot) html].

Correlation of Barley Varieties Grown Under Regular and Drought GrowthConditions

Experimental Procedures Analyzed Barley Tissues—

Four tissues [leaf, meristem, spike and root tip] at two developmentalstages, representing different plant characteristics, were sampled andRNA was extracted as described above. Each micro-array expressioninformation tissue type has received a Set ID as summarized in Table 21below.

TABLE 21 Barley transcriptome expression sets Expression Set Set IDbooting spike drought 1 leaf drought reproductive 2 leaf droughtvegetative 3 meristems drought vegetative 4 root tip drought vegetative5 root tip drought-recovery vegetative 6 Table 21: Provided are thebarley transcriptome expression sets.

Barley Yield Components and Vigor Related Parameters Assessment—

15 Barley accessions in 5 repetitive blocks, each containing 5 plantsper pot were grown at net house. Two different treatments were applied:plants were regularly fertilized and watered during plant growth untilharvesting (as recommended for commercial growth) or under droughtstress. Plants were phenotyped on a daily basis following the standarddescriptor of barley [Table 22 (below). Harvest was conducted while allthe spikes were dry. All material was oven dried and the seeds werethreshed manually from the spikes prior to measurement of the seedcharacteristics (weight and size) using scanning and image analysis. Theimage analysis system included a personal desktop computer (Intel P4 3.0GHz processor) and a public domain program—ImageJ 1.37 (Java based imageprocessing program, which was developed at the U.S. National Institutesof Health and freely available on the internet [Hypertext TransferProtocol://rsbweb (dot) nih (dot) gov/]. Next, analyzed data was savedto text files and processed using the JMP statistical analysis software(SAS institute).

Grains Number—

The total number of grains from all spikes that were manually threshedwas counted. No of grains per plot were counted

Grain Weight (Gr.)—

At the end of the experiment all spikes of the pots were collected. Thetotal grains from all spikes that were manually threshed were weight.The grain yield was calculated by per plot.

Spike Length and Width Analysis—

At the end of the experiment the length and width of five chosen spikesper plant were measured using measuring tape excluding the awns.

Spike Number Analysis—

The spikes per plant were counted.

Plant Height—

Each of the plants was measured for its height using measuring tape.Height was measured from ground level to top of the longest spikeexcluding awns at two time points at the Vegetative growth (30 daysafter sowing) and at harvest.

Heading Date—

Each of the plants was monitored for flowering date. Heading date wascalculated from sowing date till 50% of the spikes emerged.

Spike Weight—

The biomass and spikes weight of each plot was separated, measured anddivided by the number of plants.

Dry weight=total weight of the vegetative portion above ground(excluding roots) after drying at 70° C. in oven for 48 hours at twotime points at the Vegetative growth (30 days after sowing) and atharvest.

Root dry weight=total weight of the root portion underground afterdrying at 70° C. in oven for 48 hours at harvest.

Root/Shoot Ratio—

The Root/Shoot Ratio was calculated using Formula XII.Root/Shoot Ratio=total weight of the root at harvest/total weight of thevegetative portion above ground at harvest.  Formula XII

Total No of Tillers—

all tillers were counted per plot at two time points at the Vegetativegrowth (30 days after sowing) and at harvest

SPAD—

Chlorophyll content was determined using a Minolta SPAD 502 chlorophyllmeter and measurement was performed at time of flowering. SPAD meterreadings were done on young fully developed leaf. Three measurements perleaf were taken per plot.

Root FW (Gr.), Root Length (cm) and No. of Lateral Roots—

3 plants per plot were selected for measurement of root weight, rootlength and for counting the number of lateral roots formed.

Shoot FW—

weight of 3 plants per plots were recorded at different timepoints.

Relative Water Content—

Fresh weight (FW) of three leaves from three plants each from differentseed ID is immediately recorded; then leaves are soaked for 8 hours indistilled water at room temperature in the dark, and the turgid weight(TW) was recorded. Total dry weight (DW) was recorded after drying theleaves at 60° C. to a constant weight. Relative water content (RWC) wascalculated according to the following Formula I(RWC=[(FW−DW)/(TW−DW)]×100) as described above.

Harvest Index (for Barley)—

The harvest index was calculated using Formula XI above [Average spikedry weight per plant/(Average vegetative dry weight per plant+Averagespike dry weight per plant)].

Growth Rate:

the growth rate (GR) of Plant Height (Formula V above), SPAD (FormulaXIII below) and number of tillers (Formula XIV below) were calculatedwith the indicated Formulas.Growth rate of SPAD=Regression coefficient of SPAD measurements alongtime course.  Formula XIIIGrowth rate of Number of tillers=Regression coefficient of Number oftillers along time course.  Formula XIV

TABLE 22 Barley correlated parameters (vectors) Correlated parameterwith Correlation ID Chlorophyll levels 1 Dry weight harvest 2 Dry weightvegetative growth 3 Fresh weight 4 Grain number 5 Grain weight 6 Harvestindex 7 Heading date 8 Height growth rate 9 Number of tillers growthrate 10 Plant height 11 RBiH/BiH 12 Relative water content 13 Root dryweight 14 Root fresh weight 15 Root length 16 SPAD growth rate 17 Spikelength 18 Spike number 19 Spike weight per plant 20 Spike width 21Tillers number 22 lateral root number 23 Table 22: Provided are theBarley correlated parameters.

Experimental Results

Fifteen different Barley accessions were grown and characterized fordifferent parameters as described above. The average for each of themeasured parameter was calculated using the JMP software and values aresummarized in Tables 23-24 below. Subsequent correlation analysisbetween the various transcriptome sets (Table 21) and the averageparameters (Tables 23-24) was conducted. Follow, results were integratedto the database.

TABLE 23 Measured parameters of correlation IDs In Barley accessionsEcotype/ Treatment Line-1 Line-2 Line-3 Line-4 Line-5 Line-6 Line-7Line-8 1 41.33 33.57 36.57 40.50 45.07 39.73 38.33 36.17 2 6.15 5.053.20 3.28 4.76 3.55 4.52 3.38 3 0.21 0.21 0.17 4 1.90 1.52 1.17 1.951.90 1.22 1.75 1.58 5 170.00 267.50 111.00 205.33 153.60 252.50 288.40274.50 6 5.55 9.80 3.55 7.20 5.28 7.75 9.92 10.25 7 0.47 0.66 0.53 0.690.53 0.69 0.69 0.75 8 75.00 71.00 65.00 66.75 90.00 90.00 9 0.27 0.860.73 0.88 0.40 0.94 0.70 0.71 10 0.07 0.10 0.06 0.07 0.16 0.06 0.10 0.0511 46.00 52.80 35.00 38.00 45.20 48.00 37.67 41.20 11 46.00 52.80 35.0038.00 45.20 48.00 37.67 41.20 12 0.01 0.01 0.01 0.01 0.03 0.02 0.01 0.0113 80.60 53.40 55.87 43.21 69.78 45.49 76.51 14 77.52 60.19 27.13 18.62117.42 70.72 37.34 25.56 15 2.07 1.48 1.12 1.87 1.67 1.68 1.62 0.85 1621.67 20.33 22.00 24.00 20.67 18.33 21.00 20.33 17 0.09 −0.12 0.00 0.010.04 −0.07 0.01 0.00 18 16.70 16.85 13.27 13.55 14.19 15.64 15.66 17.4919 4.20 4.36 7.60 8.44 4.92 3.43 6.90 5.80 20 17.72 24.24 18.20 18.0019.50 15.00 23.40 28.16 21 8.64 9.07 7.82 7.32 8.74 7.62 6.98 8.05 2211.68 9.04 10.92 10.16 10.32 8.78 13.00 7.44 22 11.68 9.04 10.92 10.1610.32 8.78 13.00 7.44 23 8.33 8.67 7.33 7.67 6.67 6.67 7.67 6.67 Table23: Provided are the values of each of the parameters measured in Barleyaccessions according to the correlation identifications presented inTable 22 above.

TABLE 24 Measured parameters of correlation IDs in additional Barleyaccessions Ecotype/ Treat- Line- Line- Line- Line- Line- Line- Line-ment 9 10 11 12 13 14 15 1 42.13 31.77 33.47 42.37 42.27 36.77 40.63 25.67 3.31 2.65 5.12 6.86 3.11 3.74 3 0.25 0.13 0.19 0.22 4 1.88 1.731.00 0.90 0.90 1.43 0.83 5 348.50 358.00 521.39 71.50 160.13 376.67105.00 6 8.50 14.03 17.52 2.05 5.38 11.00 2.56 7 0.60 0.81 0.87 0.290.44 0.78 0.41 8 90.00 90.00 81.60 90.00 9 0.77 0.80 0.92 0.39 0.88−0.13 0.20 10 0.10 0.06 0.06 0.18 0.15 0.02 0.44 11 40.80 49.86 43.0047.40 64.80 52.60 32.00 11 40.80 49.86 43.00 47.40 64.80 52.60 32.00 120.01 0.01 0.02 0.02 0.01 0.01 0.03 13 87.41 58.32 80.58 73.09 14 66.1822.13 41.12 116.95 84.10 37.46 98.86 15 1.45 1.38 0.82 0.58 0.63 1.070.70 16 21.67 19.67 16.67 17.00 15.17 27.00 15.00 17 −0.06 0.04 0.050.00 −0.07 0.03 −0.06 18 16.00 18.31 17.42 14.23 14.81 16.54 12.72 198.55 9.67 5.42 3.05 4.07 3.72 3.21 20 21.96 33.03 34.80 11.73 18.7821.00 9.88 21 6.06 6.73 9.55 7.84 7.81 8.35 5.47 22 13.92 11.00 6.788.45 9.15 5.12 16.13 22 13.92 11.00 6.78 8.45 9.15 5.12 16.13 23 6.008.67 7.67 6.33 7.00 7.00 6.67 Table 24: Provided are the values of eachof the parameters measured in Barley accessions according to thecorrelation identifications presented in Table 22 above.

TABLE 25 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tisses and the phenotypicperformance of maintenance of performance under drought conditionsacross barley varieties Gene P Exp. Corr. Gene P Exp. Corr. Name R valueset Set ID Name R value set Set ID LYM320 0.76 8.01E−02 1 10 LYM320 0.753.09E−02 3 10 LYM320 0.82 1.18E−02 3 11 LYM320 0.81 2.60E−02 2 5 LYM3200.82 2.38E−02 2 6 LYM320 0.81 8.20E−03 4 10 LYM320 0.71 3.12E−02 4 11LYM332 0.92 8.49E−03 1 11 LYM332 0.77 7.51E−02 1 20 LYM332 0.79 1.19E−026 7 LYM332 0.83 5.18E−03 6 5 LYM332 0.84 4.14E−03 6 6 LYM332 0.742.18E−02 6 20 LYM332 0.82 1.29E−02 5 10 LYM332 0.74 3.66E−02 5 2 LYM3320.83 6.05E−03 4 19 LYM90 0.74 3.50E−02 3 19 LYM90 0.74 5.81E−02 2 22LYM90 0.85 7.72E−03 5 19 LYM90 0.73 3.80E−02 5 20 LYM91 0.79 6.25E−02 116 LYM91 0.95 3.06E−03 1 1 LYM91 0.75 1.96E−02 6 19 WYM1 0.71 4.85E−02 321 WYM1 0.71 4.77E−02 3 11 WYM1 0.76 3.03E−02 3 14 WYM1 0.85 1.58E−02 216 WYM1 0.73 6.27E−02 2 1 WYM1 0.77 2.46E−02 5 5 WYM1 0.72 4.54E−02 5 9WYM1 0.88 3.70E−03 5 12 WYM1 0.75 8.64E−02 5 8 WYM11 0.75 8.40E−02 1 21WYM11 0.81 1.45E−02 3 19 WYM11 0.78 2.10E−02 5 19 WYM11 0.72 4.28E−02 517 WYM12 0.73 9.61E−02 1 10 WYM12 0.74 8.96E−02 1 22 WYM12 0.82 4.55E−021 16 WYM12 0.95 4.35E−03 1 12 WYM12 0.97 1.67E−03 1 2 WYM12 0.996.17E−05 1 14 WYM12 0.75 3.36E−02 3 21 WYM12 0.87 1.13E−02 6 8 WYM120.83 1.97E−02 2 5 WYM12 0.89 7.39E−03 2 12 WYM12 0.72 4.60E−02 5 21WYM12 0.76 2.86E−02 5 12 WYM12 0.70 7.98E−02 4 8 WYM13 0.86 2.80E−02 118 WYM13 0.86 2.91E−02 1 20 WYM13 0.70 7.76E−02 2 18 WYM13 0.73 3.87E−025 12 WYM15 0.73 1.02E−01 1 16 WYM15 0.92 1.14E−03 3 19 WYM15 0.734.03E−02 3 20 WYM15 0.90 8.49E−04 4 19 WYM16 0.83 1.07E−02 3 19 WYM160.72 4.39E−02 3 22 WYM16 0.71 7.67E−02 2 5 WYM16 0.75 5.45E−02 2 6 WYM160.72 4.50E−02 5 19 WYM16 0.83 1.11E−02 5 17 WYM16 0.89 1.43E−03 4 19WYM17 0.72 1.09E−01 1 20 WYM17 0.70 1.18E−01 5 13 WYM17 0.71 4.75E−02 520 WYM17 0.76 4.53E−02 4 13 WYM17 0.83 5.94E−03 4 14 WYM17 0.73 6.26E−024 8 WYM18 0.98 6.88E−04 1 16 WYM18 0.71 1.16E−01 1 1 WYM18 0.85 7.62E−033 12 WYM18 0.79 1.88E−02 3 14 WYM18 0.83 2.12E−02 2 16 WYM18 0.722.80E−02 4 12 WYM19 0.72 6.78E−02 3 8 WYM19 0.81 2.75E−02 6 13 WYM2 0.824.80E−02 1 21 WYM20 0.79 1.89E−02 3 21 WYM20 0.72 7.04E−02 2 16 WYM30.75 5.12E−02 6 13 WYM4 0.74 9.36E−02 1 23 WYM4 0.87 2.49E−02 1 17 WYM40.71 7.28E−02 2 16 WYM4 0.74 2.13E−02 4 16 WYM4 0.85 3.87E−03 4 15 WYM70.74 9.53E−02 1 23 WYM7 0.70 1.19E−01 1 17 WYM7 0.74 3.72E−02 3 15 WYM80.74 9.05E−02 1 16 WYM8 0.77 2.69E−02 3 2 WYM8 0.73 4.12E−02 3 14 WYM90.71 7.10E−02 3 13 WYM9 0.78 3.85E−02 2 7 WYM9 0.71 7.63E−02 2 5 WYM90.83 1.98E−02 2 6 WYM9 0.79 3.42E−02 2 11 WYM9 0.71 7.41E−02 2 17 WYM90.86 1.27E−02 2 20 Table 25: Correlations (R) between the genesexpression levels in various tissues and the phenotypic performance.“Corr. ID” - correlation set ID according to the correlated parametersTable 22 above. “Exp. Set” - Expression set. “R” = Pearson correlationcoefficient; “P” = p value.

Example 7 Production of Maize Transcriptome and High ThroughputCorrelation Analysis with Yield Related Parameters when Grown UnderNormal Using 60K Maize Oligonucleotide Micro-Arrays

Correlation of Maize Hybrids and its Parents Grown Under NormalConditions—

50 maize hybrids and their 14 parental lines were grown in 5 repetitiveplots, in field. Maize seeds were planted and plants were grown in thefield using commercial fertilization and irrigation protocols. In orderto define correlations between the levels of RNA expression with yieldcomponents or vigor related parameters, 50 maize hybrids and their 14maize parents were analyzed and were selected for RNA expressionanalysis. The correlation between the RNA levels and the characterizedparameters was analyzed using Pearson correlation test [HypertextTransfer Protocol://World Wide Web (dot) davidmlane (dot)com/hyperstat/A34739 (dot) html].

Analyzed Maize Tissues—

All total of 64 selected maize lines were sampled. Plant tissues[leaves, stem, stem elongating internodes, female meristem] were sampledand RNA was extracted as described above. Each micro-array expressioninformation tissue type has received a Set ID as summarized in Table 26below.

TABLE 26 Maize transcriptome expression sets Expression Set Set IDheterosis flower female meristem:normal: 1 heterosis leaf:normal: 2heterosis stem:normal: 3 heterosis stem elongating internodes:normal: 4Table 26: Provided are the maize transcriptome expression sets

The following parameters were collected either by sampling 6 plants perplot or by measuring the parameter across all the plants within theplot.

Grain Weight Per Plant (Kg.)—

At the end of the experiment all ears from plots were collected, 6 earswere separately threshed and grains were weighted, all additional earswere threshed together and weighted as well. The average grain weightper ear was calculated by dividing the total grain weight by number oftotal ears per plot (based on plot). In case of 6 ears, the total grainsweight of 6 ears was divided by 6.

Ear Weight Per Plant (Gr.)—

At the end of the experiment (when ears were harvested) total and 6selected ears per plots within blocks were collected separately. Theplants with (total and 6) were weighted (Gr.) separately and the averageear per plant was calculated.

Plant Height and Ear Height—

Plants were characterized for height at harvesting. In each measure, 6plants were measured for their height using a measuring tape. Height wasmeasured from ground level to top of the plant below the tassel. Earheight was measured from the ground level to the place were the main earis located.

Average Dry Weight—

At the end of the experiment (when Inflorescence were dry) allvegetative material from plots were collected.

Cob Width [cm]—

The width of the cob without grains was measured using a caliper.

Total dry matter=total weight of the vegetative portion above ground(including ears, excluding roots).

Filled/Whole Ear—

was calculated as the length of the ear with grains out of the totalear.

Ear Row Num—

The number of rows in each ear was counted.

Stalk Width [cm]—

The diameter of the stalk was measured in the internode located belowthe main ear. Measurement was performed in 6 plants per each plot.

Leaf area index [LAI]=total leaf area of all plants in a plot.Measurement was performed using a Leaf area-meter.

1000 Grain Weight—

At the end of the experiment all seeds from all plots were collected andweighed and the weight of 1000 was calculated.

Plant Height Growth:

the growth rate (GR) of Plant Height was calculated using Formula V(described above).

Leaf Growth:

the growth rate (GR) of leaf number was calculated using Formula VI(described above).

Harvest Index—

The harvest index was calculated using Formula X above [Average graindry weight per Ear/(Average vegetative dry weight per Ear+Average Eardry weight)].

Heading Date—

Each of the plants was monitored for flowering date. Heading date wascalculated from sowing date till 50% of the male flowering.

Number Days to Silk Emergence—

Each of the plots was monitored for Silk emergence date. Number days toSilk emergence was calculated from sowing date till 50% of the spikesemerged.

Nodes Number—

the number of nodes was calculated from the whole plant.

The following parameters were collected using digital imaging system:

Grain Area (cm²)—

At the end of the growing period the grains were separated from the ear.A sample of ˜200 grains were weighted, photographed and images wereprocessed using the below described image processing system. The grainarea was measured from those images and was divided by the number ofgrains.

Grain Length and Grain Width (mm)—

At the end of the growing period the grains were separated from the ear.A sample of ˜200 grains were weighted, photographed and images wereprocessed using the below described image processing system. The sum ofgrain lengths/or width (longest axis) was measured from those images andwas divided by the number of grains.

Grain Perimeter (cm)—

At the end of the growing period the grains were separated from the ear.A sample of ˜200 grains were weight, photographed and images wereprocessed using the below described image processing system. The sum ofgrain perimeter was measured from those images and was divided by thenumber of grains.

Ear Area (cm²)—

At the end of the growing period 6 ears were, photographed and imageswere processed using the below described image processing system. TheEar area was measured from those images and was divided by the number ofEars.

Ear Filled Grain Area—

At the end of the growing period 6 ears were, photographed and imageswere processed using the below described image processing system. TheEar filled grain area was the ear with grains out of the total ear andwas measured from those images and was divided by the number of Ears.

Ear Length, Width and Perimeter (cm)—

At the end of the growing period 6 ears were, photographed and imageswere processed using the below described image processing system. TheEar length, width and perimeter were measured from those images and wasdivided by the number of ears.

The image processing system was used, which consists of a personaldesktop computer (Intel P4 3.0 GHz processor) and a public domainprogram—ImageJ 1.37, Java based image processing software, which wasdeveloped at the U.S. National Institutes of Health and is freelyavailable on the internet at Hypertext Transfer Protocol://rsbweb (dot)nih (dot) gov/. Images were captured in resolution of 10 Mega Pixels(3888×2592 pixels) and stored in a low compression JPEG (JointPhotographic Experts Group standard) format. Next, image processingoutput data for seed area and seed length was saved to text files andanalyzed using the JMP statistical analysis software (SAS institute).

TABLE 27 Maize correlated parameters (vectors) Correlated parameter withCorrelation ID 1000 grains weight 1 Average plant DW 2 Cob width 3 EarArea 4 Ear Filled Grain Area 5 Ear Perimeter 6 Ear Width 7 Ear height 8Ear length 9 Ear row num 10 Ears weight per plant (SP) 11 Filled/WholeEar 12 Grain Perimeter 13 Grain area 14 Grain length 15 Grain width 16Grains weight per plant (SP) 17 Harvest index 18 LAI 19 Leaf growth 20Nodes number 21 Num days to Heading (field) 22 Num days to Silkemergence (field) 23 Plant height 24 Plant height growth 75 Stalk width26 Total dry matter (SP) 27 Table 27: Provided are the maize correlatedparameters.

Tables 28-35 provide the measured parameters.

TABLE 28 Measured parameters in Maize accessions under normal conditionsEcotype/ Treatment Line-1 Line-2 Line-3 Line-4 Line-5 Line-6 Line-7Line-8 1 190.51 257.18 258.98 258.68 247.49 318.04 236.54 250.32 2 0.040.09 0.11 0.10 0.11 0.10 0.09 0.10 3 19.52 23.92 24.42 23.83 24.27 22.3224.14 22.45 4 33.83 61.12 73.65 58.86 63.71 85.51 81.02 63.51 5 32.0757.95 70.32 55.76 59.91 83.74 77.89 60.15 6 30.90 43.75 49.35 42.3144.59 54.27 55.12 44.79 7 3.63 4.64 4.73 4.80 4.74 5.06 4.82 4.68 853.17 94.30 116.40 95.20 108.23 99.50 85.33 119.53 9 11.79 16.89 19.6415.89 17.46 20.96 21.01 17.78 10 11.56 13.33 14.87 13.50 14.40 12.6714.07 14.47 11 0.05 0.14 0.16 0.13 0.14 0.17 0.15 0.14 12 0.94 0.95 0.950.95 0.94 0.98 0.96 0.94 13 2.62 3.20 3.14 3.19 3.12 3.35 3.10 3.10 140.47 0.68 0.65 0.68 0.65 0.75 0.62 0.64 15 0.82 1.05 1.06 1.05 1.05 1.111.02 1.06 16 0.72 0.82 0.78 0.82 0.79 0.86 0.77 0.76 17 0.05 0.09 0.110.08 0.10 0.12 0.10 0.10 18 46.99 45.42 47.01 42.40 44.89 52.35 50.7946.04 19 2875.33 5230.00 5543.00 5524.83 5515.33 5863.50 5537.17 6546.1720 0.20 0.26 0.28 0.29 0.26 0.27 0.25 0.33 21 3.44 4.90 5.60 4.47 5.574.83 4.13 5.53 22 46.00 42.00 42.00 41.67 45.00 45.00 43.00 47.60 2346.00 45.00 45.00 43.50 45.00 45.00 46.00 45.00 24 152.22 234.18 254.80238.93 241.08 238.43 225.10 256.28 25 4.53 7.38 7.75 8.07 7.29 7.67 6.948.80 26 19.12 23.25 23.22 22.86 24.09 24.23 23.71 22.75 27 0.52 1.211.50 1.24 1.35 1.44 1.29 1.29 Table 28: Correlation IDs: 1, 2, 3, 4, 5,. . . etc. refer to those described in Table 27 above [Maize correlatedparameters (vectors)].

TABLE 29 Measured parameters in Maize accessions under normal conditionsEcotype Treatment Line-9 Line-10 Line-11 Line-12 Line-13 Line-14 Line-15Line-16 1 280.76 169.91 255.84 213.97 264.06 253.92 284.00 221.00 2 0.090.06 0.10 0.13 0.11 0.12 0.11 0.11 3 26.97 21.72 24.13 22.20 24.56 23.6923.81 23.21 4 57.70 27.36 63.38 53.07 78.65 76.72 76.57 63.37 5 52.9226.33 57.48 41.25 74.89 75.09 69.95 57.74 6 41.33 29.58 45.78 46.4253.45 50.69 52.89 46.42 7 4.86 3.70 4.54 3.87 4.89 4.80 4.70 4.44 8101.93 74.67 80.80 120.07 102.46 110.30 100.83 124.33 9 15.47 9.14 18.0117.41 20.52 19.72 20.76 18.45 10 14.63 13.13 14.17 12.96 13.88 14.3713.41 15.03 11 0.13 0.05 0.12 0.08 0.15 0.15 0.13 0.12 12 0.90 0.94 0.900.74 0.95 0.98 0.89 0.89 13 3.29 2.65 3.13 2.77 3.19 3.13 3.21 3.03 140.71 0.46 0.65 0.52 0.68 0.64 0.69 0.60 15 1.13 0.84 1.02 0.93 1.07 1.051.04 1.01 16 0.80 0.70 0.81 0.70 0.80 0.77 0.84 0.75 17 0.09 0.04 0.070.05 0.11 0.10 0.09 0.08 18 43.17 37.90 42.30 27.73 45.90 45.17 43.2736.54 19 5916.33 3426.67 5848.33 4930.83 6303.17 5042.33 5144.17 6057.3320 0.27 0.25 0.25 0.24 0.26 0.26 0.25 0.23 21 5.10 4.27 4.17 6.50 5.085.13 4.40 5.30 22 41.67 41.60 42.00 45.50 45.00 42.00 45.00 45.33 2347.20 53.00 45.00 45.00 45.25 45.50 48.00 46.00 24 225.08 191.73 231.07237.17 242.83 246.03 254.93 260.87 25 7.07 5.71 6.58 6.18 7.03 7.15 7.857.70 26 22.16 19.09 23.23 23.05 22.29 23.54 22.34 22.94 27 1.16 0.611.19 1.17 1.42 1.49 1.34 1.27 Table 29: Correlation IDs: 1, 2, 3, 4, 5,. . . etc. refer to those described in Table 27 above [Maize correlatedparameters (vectors)].

TABLE 30 Measured parameters in Maize accessions under normal conditionsEcotype Treatment Line-17 Line-18 Line-19 Line-20 Line-21 Line-22Line-23 Line-24 1 205.45 227.12 264.61 219.47 245.06 224.95 275.42262.93 2 0.13 0.11 0.12 0.13 0.11 0.08 0.09 0.10 3 22.67 22.24 26.0624.58 24.83 23.39 24.22 24.32 4 59.16 66.15 73.40 69.68 67.24 43.5155.21 55.49 5 56.29 62.09 68.49 67.66 61.63 39.49 53.28 53.33 6 43.7851.44 50.92 48.58 46.61 35.27 40.79 45.11 7 4.40 4.31 4.74 4.59 4.644.25 4.72 4.67 8 126.97 123.37 90.00 131.89 135.97 97.00 105.67 102.33 917.31 19.43 20.02 19.01 18.32 13.20 14.88 15.25 10 14.61 13.91 15.3016.13 15.61 14.26 15.00 14.50 11 0.12 0.12 0.14 0.14 0.15 0.08 0.15 0.1312 0.95 0.90 0.93 0.97 0.90 0.90 0.96 0.96 13 2.94 3.04 3.25 2.95 3.032.91 3.20 3.29 14 0.57 0.61 0.68 0.57 0.60 0.56 0.67 0.69 15 1.01 1.031.09 1.02 1.04 0.95 1.08 1.12 16 0.71 0.75 0.79 0.70 0.72 0.75 0.79 0.7917 0.08 0.10 0.11 0.11 0.09 0.05 0.09 0.10 18 36.76 41.35 42.83 43.8943.43 37.89 48.12 46.48 19 6247.50 5918.00 5621.75 6480.33 6408.174056.67 5556.50 4626.50 20 0.31 0.29 0.23 0.33 0.26 0.23 0.29 0.29 216.53 5.71 4.25 6.05 6.27 5.23 4.83 5.17 22 40.75 41.00 38.33 40.00 42.0040.80 44.33 42.00 23 45.00 48.00 48.00 41.33 41.00 41.33 41.40 45.25 24260.30 255.79 233.72 264.12 266.64 204.50 249.67 237.17 25 8.04 8.116.48 8.19 7.38 5.96 7.51 7.41 26 24.58 23.27 24.68 25.08 23.13 20.7921.13 20.63 27 1.37 1.29 1.40 1.47 1.41 0.92 1.28 1.22 Table 30.Correlation IDs: 1, 2, 3, 4, 5, . . . etc. refer to those described inTable 27 above [Maize correlated parameters (vectors)].

TABLE 31 Measured parameters in Maize accessions under normal conditionsEcotype Treatment Line-25 Line-26 Line-27 Line-28 Line-29 Line-30Line-31 Line-32 1 245.85 262.71 239.16 255.66 303.25 214.93 228.10254.51 2 0.10 0.13 0.11 0.09 0.14 0.10 0.14 0.11 3 23.69 24.03 24.0523.29 24.80 24.66 25.13 26.11 4 68.01 60.04 73.03 58.82 94.18 69.4473.03 65.02 5 62.50 56.82 69.42 56.12 90.14 64.64 70.46 60.11 6 46.3042.55 46.67 41.90 54.03 49.72 46.90 42.72 7 4.91 4.71 5.24 4.66 5.644.41 4.98 5.04 8 95.69 128.67 119.69 91.05 108.33 88.78 129.83 121.67 917.65 16.24 17.91 16.32 20.96 20.05 18.49 16.63 10 14.88 15.67 16.2313.63 14.67 15.33 17.17 15.47 11 0.12 0.16 0.15 0.13 0.21 0.12 0.16 0.1412 0.91 0.94 0.95 0.95 0.96 0.93 0.96 0.92 13 3.19 3.22 3.14 3.19 3.402.96 3.01 3.21 14 0.66 0.66 0.63 0.68 0.76 0.56 0.58 0.67 15 1.05 1.111.09 1.06 1.17 0.97 1.03 1.08 16 0.80 0.76 0.74 0.81 0.82 0.73 0.72 0.7917 0.09 0.11 0.10 0.09 0.12 0.08 0.11 0.09 18 42.18 44.27 44.69 47.9446.14 40.60 38.88 41.87 19 5196.50 5537.50 6175.17 5007.17 7017.004816.75 6441.83 5872.83 20 0.26 0.28 0.29 0.29 0.28 0.18 0.29 0.26 214.28 5.67 5.87 4.63 5.33 4.89 5.67 5.83 22 47.00 41.75 43.50 45.50 46.0045.00 45.00 48.50 23 41.33 45.00 48.00 45.00 45.00 48.50 45.00 42.00 24232.25 269.17 251.29 223.38 250.00 219.17 267.83 238.70 25 7.85 8.577.53 7.65 7.95 5.08 8.13 7.29 26 21.52 22.55 22.96 21.70 24.87 24.0524.16 22.00 27 1.24 1.57 1.44 1.19 1.86 1.13 1.61 1.37 Table 31:Correlation IDs: 1, 2, 3, 4, 5, . . . etc. refer to those described inTable 27 above [Maize correlated parameters (vectors)].

TABLE 32 Measured parameters in Maize accessions under normal conditionsEcotype Treatment Line-33 Line-34 Line-35 Line-36 Line-37 Line-38Line-39 Line-40 1 213.20 284.32 233.47 236.14 190.80 221.89 189.77209.58 2 0.11 0.11 0.11 0.11 0.12 0.12 0.12 0.10 3 25.25 25.19 24.5326.04 26.57 25.71 23.73 23.75 4 66.12 85.22 67.49 66.13 63.71 84.6161.91 57.69 5 62.19 81.10 65.83 61.12 60.01 81.22 58.40 55.27 6 46.0955.31 46.40 47.32 44.34 52.18 43.42 42.21 7 4.70 5.26 4.77 4.94 4.615.10 4.59 4.51 8 102.93 96.50 93.92 106.39 108.00 111.50 132.33 100.67 918.01 20.42 17.67 17.60 17.31 20.82 17.27 16.55 10 15.53 14.00 14.6716.67 17.17 16.67 16.57 13.89 11 0.14 0.17 0.14 0.14 0.14 0.18 0.12 0.1212 0.94 0.95 0.97 0.92 0.94 0.96 0.94 0.96 13 2.95 3.21 3.11 3.04 2.813.11 2.81 2.93 14 0.57 0.69 0.63 0.61 0.51 0.62 0.51 0.57 15 1.02 1.091.04 1.05 0.98 1.08 0.97 0.98 16 0.71 0.81 0.77 0.73 0.66 0.73 0.66 0.7417 0.08 0.11 0.10 0.10 0.08 0.12 0.08 0.09 18 40.79 47.36 42.93 40.9638.94 47.25 38.09 43.84 19 5230.50 6099.50 4960.17 5974.33 6490.257194.50 6731.00 5271.83 20 0.26 0.30 0.28 0.15 0.30 0.25 0.30 0.29 216.07 5.17 4.83 5.17 6.08 5.25 6.23 5.22 22 48.00 49.00 46.00 48.20 48.0045.33 55.00 45.20 23 45.50 48.00 45.50 48.33 47.00 47.00 48.00 45.33 24217.45 232.17 240.46 247.39 238.08 265.42 263.90 237.72 25 6.13 7.907.02 6.13 7.22 7.27 7.74 7.34 26 24.83 24.59 24.51 24.60 25.22 25.4423.67 22.36 27 1.33 1.51 1.37 1.34 1.39 1.64 1.29 1.21 Table 32.Correlation IDs: 1, 2, 3, 4, 5, . . . etc. refer to those described inTable 27 above [Maize correlated parameters (vectors)].

TABLE 33 Measured parameters in Maize accessions under normal conditionsEcotype Treatment Line-41 Line-42 Line-43 Line-44 Line-45 Line-46Line-47 Line-48 1 163.36 162.24 204.98 234.99 244.33 237.54 212.39 96.702 0.11 0.14 0.13 0.16 0.12 0.12 0.05 0.09 3 22.88 23.40 26.01 26.6426.55 21.63 21.76 17.21 4 57.08 57.70 72.64 77.81 72.24 44.63 39.6127.53 5 55.46 54.92 68.86 72.94 68.58 41.47 37.69 24.47 6 44.25 41.4448.09 49.39 45.18 35.50 34.49 31.43 7 4.04 4.34 4.90 5.08 5.27 4.06 3.632.81 8 152.87 152.97 115.79 140.56 117.96 130.46 45.17 122.03 9 17.5816.66 19.06 19.42 17.57 13.65 13.48 12.24 10 16.03 16.77 16.50 16.7916.83 13.13 13.32 12.20 11 0.11 0.11 0.15 0.18 0.16 0.07 0.07 0.03 120.97 0.94 0.95 0.92 0.95 0.92 0.93 0.88 13 2.55 2.69 3.04 3.10 3.17 2.852.71 2.02 14 0.43 0.47 0.60 0.62 0.64 0.54 0.51 0.27 15 0.88 0.92 1.031.08 1.11 0.94 0.86 0.69 16 0.62 0.65 0.73 0.73 0.73 0.73 0.74 0.50 170.08 0.07 0.10 0.12 0.10 0.05 0.04 0.01 18 39.50 33.74 42.36 39.27 43.5429.73 47.67 16.59 19 6063.00 7723.00 6796.33 8181.75 5685.67 4841.173036.33 4221.83 20 0.32 0.24 0.18 0.25 0.22 0.26 0.21 0.22 21 7.17 6.975.42 6.50 5.54 6.17 3.03 6.97 22 42.00 45.00 42.00 45.00 43.50 46.0048.67 44.25 23 53.00 45.00 54.50 48.00 46.00 54.00 47.33 45.00 24 270.13289.47 264.62 278.94 250.33 249.83 151.63 213.21 25 8.45 7.54 6.72 7.575.98 5.97 4.66 6.03 26 23.36 24.72 24.56 26.62 23.10 21.21 20.18 21.4227 1.21 1.34 1.49 1.86 1.48 1.16 0.63 0.69 Table 33. Correlation IDs: 1,2, 3, 4, 5, . . . etc. refer to those described in Table 27 above [Maizecorrelated parameters (vectors)].

TABLE 34 Measured parameters in Maize accessions under normal conditionsEcotype/ Line- Line- Line- Treatment 49 50 Line-51 Line-52 53 Line-54Line-55 Line-56 1 261.45 247.02 226.98 229.90 223.89 266.77 247.68212.41 2 0.07 0.12 0.12 0.08 0.13 0.11 0.12 0.11 3 16.47 22.15 21.2816.89 24.28 24.82 24.44 25.20 4 40.38 72.46 84.80 27.60 65.29 72.9769.25 71.51 5 30.89 70.21 83.08 18.69 58.53 68.17 62.29 65.30 6 42.6653.45 56.32 29.01 50.34 51.55 47.17 49.75 7 3.24 4.42 4.60 3.05 4.254.92 4.79 4.68 8 92.03 129.67 103.28 82.54 100.40 101.33 106.90 125.78 916.57 20.41 23.01 11.42 19.50 18.52 18.56 19.26 10 9.95 13.94 13.67 6.7114.19 15.17 14.75 16.30 11 0.05 0.15 0.15 0.03 0.10 0.17 0.13 0.12 120.73 0.97 0.98 0.65 0.89 0.93 0.87 0.90 13 2.93 3.10 3.02 2.57 2.90 3.203.13 2.97 14 0.58 0.63 0.60 0.45 0.56 0.67 0.64 0.57 15 0.94 1.05 1.010.81 0.95 1.08 1.03 1.01 16 0.78 0.76 0.75 0.70 0.75 0.78 0.79 0.71 170.02 0.10 0.11 0.01 0.07 0.09 0.07 0.09 18 30.03 43.39 46.96 12.14 32.8244.89 37.82 43.41 19 3521.17 6460.17 5934.17 3966.17 5898.00 6248.835150.67 6197.83 20 0.19 0.27 0.25 0.15 0.18 0.26 0.21 0.25 21 4.73 5.894.72 5.79 4.80 4.44 5.13 5.17 22 23 46.00 46.00 44.50 47.00 45.00 45.6747.33 49.00 24 204.70 266.94 249.50 195.96 244.73 264.39 251.72 277.0025 5.63 7.75 7.49 3.64 5.70 7.28 6.55 7.63 26 19.18 23.09 24.67 21.1423.81 23.46 25.20 22.17 27 0.68 1.51 1.47 0.62 1.35 1.55 1.38 1.26 Table34 Correlation IDs: 1, 2, 3, 4, 5, . . . etc. refer to those describedin Table 27 above [Maize correlated parameters (vectors)].

TABLE 35 Measured parameters in Maize accessions under normal conditionsEcotype/ Line- Line- Line- Treatment 57 58 Line-59 Line-60 61 Line-62Line-63 Line-64 1 240.39 202.45 238.09 272.16 227.76 256.12 218.50228.72 2 0.12 0.11 0.09 0.10 0.12 0.11 0.15 0.10 3 22.78 24.20 23.5423.00 23.40 25.60 24.04 25.34 4 69.09 78.70 73.52 75.59 68.66 74.9766.97 71.79 5 65.69 76.13 70.12 73.11 64.40 70.84 63.35 68.26 6 47.3350.88 51.14 53.61 47.34 47.60 52.23 47.09 7 4.85 4.80 4.70 4.62 4.725.13 4.42 4.95 8 105.95 118.02 98.23 112.54 132.73 127.80 148.60 98.10 918.18 20.37 19.59 20.48 18.87 18.59 18.91 18.11 10 15.13 15.97 13.7713.77 15.97 15.83 16.49 16.20 11 0.14 0.14 0.14 0.14 0.14 0.16 0.12 0.1412 0.93 0.97 0.95 0.97 0.93 0.94 0.94 0.94 13 3.14 2.95 3.13 3.16 3.013.18 2.89 3.00 14 0.64 0.56 0.64 0.67 0.59 0.66 0.54 0.59 15 1.04 1.011.03 1.06 1.04 1.08 1.01 1.03 16 0.78 0.70 0.78 0.80 0.72 0.77 0.68 0.7217 0.10 0.09 0.10 0.10 0.09 0.09 0.09 0.09 18 43.42 43.67 50.32 46.2940.66 44.06 36.22 46.26 19 5762.83 7229.83 5846.33 6018.67 7234.176496.17 7163.83 5400.17 20 0.24 0.30 0.26 0.27 0.31 0.26 0.20 0.27 214.93 5.80 4.80 5.04 5.60 5.87 6.50 4.97 22 23 46.67 24 249.00 253.16243.61 258.15 270.92 273.64 277.87 227.15 25 6.87 8.19 7.03 7.57 9.027.77 6.98 6.93 26 21.61 24.13 22.80 23.72 23.16 21.94 25.20 21.50 271.39 1.34 1.24 1.29 1.40 1.43 1.56 1.29 Table 35. Correlation IDs: 1, 2,3, 4, 5, . . . etc. refer to those described in Table 27 above [Maizecorrelated parameters (vectors)].

TABLE 36 Correlation between the expression level of selected genes ofsome embodiments of the invention in the various tissues and thephenotypic performance of maintenance of performance under droughtconditions across maize varieties Corr. Corr. Gene Exp. Set Gene Exp.Set Name R P value set ID Name R P value set ID WYM104 0.85 9.12E−04 423 WYM104 0.71 6.86E−05 2 18 WYM105 0.71 6.04E−04 3 18 WYM106 0.736.87E−03 4 5 WYM106 0.72 8.70E−03 4 17 WYM106 0.73 7.56E−03 4 11 WYM1060.71 9.85E−03 4 12 WYM106 0.74 6.40E−03 4 10 WYM106 0.81 1.27E−03 4 18WYM106 0.75 5.38E−03 4 7 WYM106 0.71 9.56E−03 4 3 WYM107 0.72 8.42E−03 45 WYM107 0.78 2.50E−03 4 17 WYM107 0.78 2.65E−03 4 11 WYM107 0.746.11E−03 4 25 WYM107 0.77 3.19E−03 4 18 WYM107 0.70 1.06E−02 4 4 WYM1070.72 8.55E−03 4 7 WYM107 0.73 7.59E−03 4 3 WYM107 0.71 9.65E−03 4 6WYM108 0.74 2.69E−04 3 18 WYM108 0.74 6.00E−03 4 25 WYM47 0.76 4.11E−034 15 WYM47 0.79 2.35E−03 4 25 WYM47 0.73 7.58E−03 4 18 WYM47 0.801.75E−03 4 14 WYM47 0.77 3.15E−03 4 13 WYM47 0.74 5.86E−03 4 7 WYM470.70 1.09E−02 4 3 WYM47 0.70 1.10E−02 4 20 WYM47 0.74 6.36E−03 4 16WYM48 0.72 8.60E−03 4 17 WYM48 0.75 5.41E−03 4 11 WYM48 0.80 1.68E−03 418 WYM48 0.72 7.99E−03 4 7 WYM48 0.74 6.01E−03 4 3 WYM55 0.74 5.92E−03 45 WYM55 0.75 5.16E−03 4 17 WYM55 0.81 1.36E−03 4 18 WYM55 0.71 9.45E−034 4 WYM55 0.75 4.99E−03 4 6 WYM56 0.73 7.04E−03 4 5 WYM56 0.83 8.09E−044 17 WYM56 0.86 3.00E−04 4 11 WYM56 0.87 2.80E−04 4 15 WYM56 0.745.74E−03 4 25 WYM56 0.75 4.73E−03 4 18 WYM56 0.83 8.97E−04 4 14 WYM560.81 1.41E−03 4 13 WYM56 0.73 6.51E−03 4 4 WYM56 0.81 1.31E−03 4 7 WYM560.81 1.57E−03 4 3 WYM56 0.77 3.43E−03 4 27 WYM56 0.78 2.52E−03 4 19WYM58 0.80 1.94E−03 4 5 WYM58 0.86 3.30E−04 4 17 WYM58 0.82 1.20E−03 411 WYM58 0.77 3.62E−03 4 15 WYM58 0.91 4.96E−05 4 18 WYM58 0.75 4.93E−034 14 WYM58 0.76 3.98E−03 4 13 WYM58 0.78 2.76E−03 4 4 WYM58 0.801.68E−03 4 7 WYM58 0.79 2.15E−03 4 3 WYM58 0.78 3.01E−03 4 6 WYM64 0.746.08E−03 4 17 WYM64 0.73 6.57E−03 4 11 WYM64 0.73 6.63E−03 4 15 WYM640.75 5.19E−03 4 18 WYM64 0.79 2.27E−03 4 14 WYM64 0.77 3.16E−03 4 13WYM64 0.73 6.63E−03 4 7 WYM64 0.76 4.17E−03 4 16 WYM67 0.75 4.59E−03 4 5WYM67 0.74 6.29E−03 4 17 WYM67 0.72 7.99E−03 4 11 WYM67 0.72 8.11E−03 418 WYM67 0.74 6.20E−03 4 4 WYM67 0.71 9.69E−03 4 3 WYM67 0.75 5.11E−03 46 WYM69 0.83 8.10E−04 4 21 WYM98 0.78 2.71E−03 4 17 WYM98 0.72 8.14E−034 11 WYM98 0.73 6.72E−03 4 15 WYM98 0.76 4.34E−03 4 25 WYM98 0.822.22E−03 4 23 WYM98 0.80 1.79E−03 4 18 WYM98 0.74 5.63E−03 4 14 WYM980.73 7.01E−03 4 13 WYM98 0.74 5.57E−03 4 7 WYM98 0.74 5.73E−03 4 3 WYM980.71 1.04E−02 4 19 Table 36. Correlations (R) between the genesexpression levels in various tissues and the phenotypic performance.“Corr. ID”—correlation set ID according to the correlated parametersTable above. “Exp. Set”—Expression set. “R” = Pearson correlationcoefficient; “P” = p value.

Example 8 Production of Brachypodium Transcriptome and High ThroughputCorrelation Analysis Using 60K Brachypodium Oligonucleotide Micro-Array

In order to produce a high throughput correlation analysis comparingbetween plant phenotype and gene expression level, the present inventorsutilized a brachypodium oligonucleotide micro-array, produced by AgilentTechnologies [Hypertext Transfer Protocol://World Wide Web (dot) chem.(dot) agilent (dot) com/Scripts/PDS (dot) asp?1Page=50879]. The arrayoligonucleotide represents about 60K brachypodium genes and transcripts.In order to define correlations between the levels of RNA expression andyield or vigor related parameters, various plant characteristics of 24different brachypodium accessions were analyzed. Among them, 22accessions encompassing the observed variance were selected for RNAexpression analysis and comparative genomic hybridization (CGH)analysis.

The correlation between the RNA levels and the characterized parameterswas analyzed using Pearson correlation test [Hypertext TransferProtocol://World Wide Web (dot) davidmlane (dot) com/hyperstat/A34739(dot) html].

Additional correlation analysis was done by comparing plant phenotypeand gene copy number. The correlation between the normalized copy numberhybridization signal and the characterized parameters was analyzed usingPearson correlation test [Hypertext Transfer Protocol://World Wide Web(dot) davidmlane (dot) com/hyperstat/A34739 (dot) html].

Experimental Procedures

Analyzed Brachypodium Tissues—

two tissues [leaf and spike] were sampled and RNA was extracted asdescribed above. Each micro-array expression information tissue type hasreceived a Set ID as summarized in Table 37 below.

TABLE 37 Brachypodium transcriptome expression sets Expression Set SetID ecotypes 753/leaf: flowering: normal: 1 ecotypes 753/spike:flowering: normal: 2 Table 37: Provided are the brachypodiumtranscriptome expression sets under normal conditions.

Brachypodium Yield Components and Vigor Related Parameters Assessment—

24 brachypodium accessions were grown in 4-6 repetitive plots (8 plantper plot), in a green house. The growing protocol was as follows:brachypodium seeds were sown in plots and grown under normal condition.Plants were continuously phenotyped during the growth period and atharvest (Table 38, below). The image analysis system included a personaldesktop computer (Intel P4 3.0 GHz processor) and a public domainprogram—ImageJ 1.37 (Java based image processing program, which wasdeveloped at the U.S. National Institutes of Health and freely availableon the internet [Hypertext Transfer Protocol://rsbweb (dot) nih (dot)gov/]. Next, analyzed data was saved to text files and processed usingthe JMP statistical analysis software (SAS institute).

At the end of the growing period the grains were separated from thespikes and the following parameters were measured using digital imagingsystem and collected:

No. of Tillering—

all tillers were counted per plant at harvest (mean per plot).

Head Number—

At the end of the experiment, heads were harvested from each plot andwere counted.

Total Grains Weight Per Plot (Gr.)—

At the end of the experiment (plant ‘Heads’) heads from plots werecollected, the heads were threshed and grains were weighted. Inaddition, the average grain weight per head was calculated by dividingthe total grain weight by number of total heads per plot (based onplot).

Highest Number of Spikelets—

The highest spikelet number per head was calculated per plant (mean perplot).

Mean Number of Spikelets—

The mean spikelet number per head was calculated per plot.

Plant Height—

Each of the plants was measured for its height using measuring tape.Height was measured from ground level to spike base of the longest spikeat harvest.

Spikelets Weight (Gr.)—

The biomass and spikes weight of each plot was separated, measured perplot.

Average Head Weight—

calculated by dividing spikelets weight with head number (Gr.).

Harvest Index—

The harvest index was calculated using Formula XV.Harvest Index(brachypodium)=Average grain weight/averagedry(vegetative+spikelet)weight per plant.  Formula XV

Spikelets Index—

The Spikelets index is calculated using Formula XVI.Spikelets Index=Average Spikelets weight per plant/(Average vegetativedry weight per plant plus Average Spikelets weight per plant).  FormulaXVI

Percent Number of Heads with Spikelets—

The number of heads with more than one spikelet per plant were countedand the percent from all heads per plant was calculated.

Total Dry Mater Per Plot—

Calculated as Vegetative portion above ground plus all the spikelet dryweight per plot.

1000 Grain Weight—

At the end of the experiment all grains from all plots were collectedand weighted and the weight of 1000 were calculated.

The following parameters were collected using digital imaging system:

At the end of the growing period the grains were separated from thespikes and the following parameters were measured and collected:

(i) Average Grain Area (cm²)—

A sample of ˜200 grains was weighted, photographed and images wereprocessed using the below described image processing system. The grainarea was measured from those images and was divided by the number ofgrains.

(ii) Average Grain Length, Perimeter and Width (cm)—

A sample of ˜200 grains was weighted, photographed and images wereprocessed using the below described image processing system. The sum ofgrain lengths and width (longest axis) was measured from those imagesand was divided by the number of grains.

The image processing system was used, which consists of a personaldesktop computer (Intel P4 3.0 GHz processor) and a public domainprogram—ImageJ 1.37, Java based image processing software, which wasdeveloped at the U.S. National Institutes of Health and is freelyavailable on the internet at Hypertext Transfer Protocol://rsbweb (dot)nih (dot) gov/. Images were captured in resolution of 10 Mega Pixels(3888×2592 pixels) and stored in a low compression JPEG (JointPhotographic Experts Group standard) format. Next, image processingoutput data for seed area and seed length was saved to text files andanalyzed using the JMP statistical analysis software (SAS institute).

TABLE 38 Brachypodium correlated parameters (vectors) Correlatedparameter with Correlation ID 1000 grain weight 1 Average head weight 2Grain Perimeter 3 Grain area 4 Grain length 5 Grain width 6 Grainsweight per plant 7 Grains weight per plot 8 Harvest index 9 Heads perplant 10 Heads per plot 11 Highest num of spikelets per plot 12 Mean numof spikelets per plot 13 Num of heads with spikelets per plant 14Percent Num of heads with spikelets 15 Plant Vegetative DW 16 Plantheight 17 Plants num 18 Spikelets DW per plant 19 Spikelets weight 20Spikes index 21 Tillering 22 Total dry mater per plant 23 Total drymater per plot 24 Vegetative DW 25 Table 38: Provided are thebrachypodium correlated parameters.

Experimental Results

25 different Brachypodium accessions were grown and characterized fordifferent parameters as described above. The average for each of themeasured parameter was calculated using the JMP software and values aresummarized in Tables 39-40 below. Subsequent correlation analysisbetween the various transcriptome sets and the average parameters wasconducted. Follow, results were integrated to the database.

TABLE 39 Measured parameters of correlation IDs in Brachypodiumaccessions under normal conditions Ecotype/ Line- Line- Treatment Line-1Line-2 Line-3 Line-4 Line-5 Line-6 Line-7 Line-8 Line-9 10 11 1 3.753.78 3.35 4.88 5.54 4.98 4.83 5.54 3.84 4.76 4.73 2 0.06 0.04 0.05 0.070.04 0.06 0.05 0.04 0.08 0.06 0.05 3 1.67 1.62 1.62 1.69 1.82 1.83 1.741.93 1.68 1.82 1.69 4 0.10 0.10 0.09 0.09 0.11 0.11 0.10 0.11 0.10 0.110.10 5 0.73 0.72 0.72 0.74 0.83 0.82 0.78 0.90 0.75 0.79 0.75 6 0.180.17 0.17 0.16 0.16 0.17 0.17 0.16 0.17 0.18 0.17 7 0.14 0.06 0.08 0.260.14 0.14 0.14 0.11 0.08 0.07 0.39 8 1.05 0.44 0.61 1.96 1.11 1.07 1.090.84 0.50 0.39 3.07 9 0.13 0.14 0.15 0.20 0.20 0.16 0.14 0.26 0.07 0.110.22 10 16.29 7.08 6.59 11.63 10.48 9.09 14.13 5.88 11.89 8.02 23.75 11121.75 56.60 52.75 83.40 82.40 70.13 110.33 47.00 81.50 48.60 185.50 123.00 2.60 3.00 2.20 2.00 2.25 1.83 2.00 3.50 2.00 2.50 13 2.10 2.10 1.721.69 1.38 1.65 1.43 1.25 2.41 1.56 1.76 14 5.27 2.50 2.06 2.08 0.71 1.941.08 0.35 7.59 1.87 4.98 15 27.61 35.33 21.67 14.00 5.42 15.42 6.40 4.5155.41 16.51 15.52 16 0.42 0.12 0.13 0.38 0.32 0.32 0.39 0.13 0.44 0.310.87 17 31.65 23.44 22.75 31.95 34.36 28.65 28.88 24.74 31.40 29.1537.30 18 7.50 8.00 8.00 7.20 7.80 7.75 7.83 8.00 6.50 6.40 7.75 19 0.960.31 0.33 0.88 0.44 0.56 0.67 0.26 0.92 0.45 1.14 20 7.18 2.50 2.68 6.423.45 4.29 5.29 2.04 6.25 2.66 8.89 21 0.71 0.72 0.73 0.71 0.58 0.66 0.640.66 0.69 0.60 0.59 22 16.84 7.20 7.00 11.97 10.67 9.38 14.58 6.35 12.388.60 25.50 23 1.38 0.43 0.47 1.25 0.76 0.88 1.06 0.38 1.36 0.76 2.01 2410.26 3.45 3.74 9.12 6.00 6.78 8.34 3.04 9.21 4.47 15.79 25 3.08 0.951.06 2.69 2.55 2.48 3.05 1.00 2.96 1.81 6.89 Table 39: Correlation IDs:1, 2, 3, 4, 5, . . . etc. refer to those described in Table 38 above[Brachypodium correlated parameters (vectors)].

TABLE 40 Measured parameters of correlation IDs in brachypodiumaccessions under normal conditions Ecotype/ Line- Line- Line- Line-Line- Line- Line- Line- Line- Line- Line- Treatment 12 13 14 15 16 17 1819 20 21 22 1 5.24 4.96 4.00 4.26 5.99 4.34 3.70 3.90 4.82 4.87 3.76 20.05 0.06 0.10 0.08 0.08 0.06 0.09 0.04 0.06 0.09 0.09 3 1.91 1.71 1.811.75 1.87 1.66 1.65 1.60 1.80 1.90 1.68 4 0.12 0.10 0.10 0.09 0.12 0.090.09 0.09 0.10 0.11 0.09 5 0.86 0.74 0.84 0.80 0.84 0.74 0.75 0.72 0.790.87 0.76 6 0.19 0.17 0.15 0.14 0.18 0.16 0.15 0.15 0.17 0.16 0.15 70.14 0.13 0.37 0.49 0.31 0.20 0.35 0.27 0.32 0.44 0.30 8 1.09 1.07 2.993.52 2.41 1.47 2.58 2.03 2.58 3.40 1.92 9 0.09 0.18 0.09 0.16 0.18 0.110.21 0.17 0.15 0.18 0.09 10 16.06 9.74 22.19 24.32 13.25 19.22 16.1121.40 25.88 17.05 25.54 11 125.00 80.75 177.50 172.80 98.60 143.17123.50 156.83 207 135 177 12 2.40 2.00 3.50 3.80 2.80 2.83 2.83 2.332.60 4.50 3.17 13 1.83 1.42 2.71 2.61 2.12 2.15 2.17 1.85 1.93 2.85 2.7914 3.70 0.89 12.58 12.13 6.35 7.15 9.44 5.02 4.90 7.72 15.36 15 20.348.11 53.21 47.81 42.81 34.92 52.40 20.84 17.55 47.73 59.01 16 0.69 0.341.72 1.32 0.48 0.63 0.82 0.67 0.87 1.05 1.73 17 45.09 22.39 55.04 45.3440.20 39.18 45.35 29.41 38.39 46.74 58.82 18 8.00 8.25 8.00 7.00 7.607.33 7.50 7.33 8.00 7.88 6.83 19 0.83 0.59 2.27 1.91 1.09 1.26 1.46 0.961.56 1.42 2.25 20 6.65 4.92 18.15 13.49 8.35 9.42 11.31 7.16 12.44 11.0515.55 21 0.54 0.68 0.56 0.59 0.70 0.66 0.68 0.60 0.65 0.57 0.57 22 16.5610.53 27.15 26.30 13.56 20.79 16.99 23.61 27.20 18.25 29.09 23 1.53 0.933.99 3.23 1.57 1.89 2.28 1.63 2.43 2.47 3.98 24 12.20 7.76 31.94 22.7812.04 14.14 17.78 12.29 19.40 19.27 27.67 25 5.55 2.84 13.80 9.28 3.704.72 6.47 5.13 6.96 8.23 12.12 Table 40: Correlation IDs: 1, 2, 3, 4, 5,. . . etc. refer to those described in Table 38 above [Brachypodiumcorrelated parameters (vectors)].

TABLE 41 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance of maintenance of performance under drought conditionsacross brachypodium ecotypes Corr. Gene Exp. Corr. Gene P Exp. Set NameR P value set Set ID Name R value set ID WYM100 0.78 7.47E−03 2 24WYM100 0.71 2.13E−02 2 19 WYM100 0.71 2.03E−02 2 7 WYM100 0.82 3.36E−032 25 WYM100 0.79 6.09E−03 2 16 WYM100 0.74 1.38E−02 2 20 WYM100 0.823.50E−03 2 17 WYM100 0.73 1.65E−02 2 8 WYM100 0.73 1.67E−02 2 2 WYM1000.75 1.24E−02 2 23 WYM101 0.86 6.31E−04 1 12 WYM101 0.72 1.24E−02 1 7WYM101 0.80 2.86E−03 1 13 WYM101 0.70 1.57E−02 1 8 WYM101 0.78 7.88E−032 7 WYM101 0.77 8.93E−03 2 8 WYM21 0.76 6.26E−03 1 7 WYM21 0.84 1.23E−031 15 WYM21 0.71 1.54E−02 1 14 WYM21 0.73 1.06E−02 1 17 WYM21 0.757.67E−03 1 8 WYM21 0.85 8.73E−04 1 2 WYM22 0.82 2.16E−03 1 7 WYM22 0.711.44E−02 1 25 WYM22 0.72 1.30E−02 1 17 WYM22 0.83 1.73E−03 1 8 WYM230.81 2.57E−03 1 11 WYM23 0.79 3.91E−03 1 22 WYM23 0.73 1.05E−02 1 19WYM23 0.88 3.22E−04 1 12 WYM23 0.72 1.22E−02 1 7 WYM23 0.73 1.11E−02 115 WYM23 0.72 1.24E−02 1 16 WYM23 0.75 8.25E−03 1 14 WYM23 0.89 2.59E−041 13 WYM23 0.83 1.59E−03 1 10 WYM23 0.73 1.04E−02 1 23 WYM24 0.841.33E−03 1 11 WYM24 0.82 2.01E−03 1 22 WYM24 0.85 1.00E−03 1 24 WYM240.87 4.23E−04 1 19 WYM24 0.89 2.05E−04 1 12 WYM24 0.92 7.82E−05 1 7WYM24 0.80 3.30E−03 1 25 WYM24 0.85 1.02E−03 1 15 WYM24 0.80 3.12E−03 116 WYM24 0.84 1.12E−03 1 14 WYM24 0.88 4.03E−04 1 20 WYM24 0.89 2.16E−041 13 WYM24 0.90 1.72E−04 1 8 WYM24 0.82 2.18E−03 1 10 WYM24 0.851.00E−03 1 2 WYM24 0.85 9.86E−04 1 23 WYM24 0.84 2.56E−03 2 11 WYM240.88 8.05E−04 2 22 WYM24 0.84 2.39E−03 2 24 WYM24 0.87 9.31E−04 2 19WYM24 0.81 4.12E−03 2 25 WYM24 0.80 5.52E−03 2 15 WYM24 0.84 2.46E−03 216 WYM24 0.88 8.44E−04 2 14 WYM24 0.85 1.68E−03 2 20 WYM24 0.73 1.64E−022 13 WYM24 0.76 1.11E−02 2 17 WYM24 0.86 1.59E−03 2 10 WYM24 0.741.45E−02 2 2 WYM24 0.86 1.36E−03 2 23 WYM25 0.72 1.16E−02 1 24 WYM250.72 1.29E−02 1 19 WYM25 0.87 5.26E−04 1 12 WYM25 0.74 8.61E−03 1 7WYM25 0.72 1.18E−02 1 25 WYM25 0.80 3.13E−03 1 15 WYM25 0.72 1.20E−02 116 WYM25 0.73 1.08E−02 1 14 WYM25 0.72 1.34E−02 1 20 WYM25 0.88 4.11E−041 13 WYM25 0.77 5.52E−03 1 17 WYM25 0.72 1.17E−02 1 8 WYM25 0.731.02E−02 1 2 WYM25 0.73 1.15E−02 1 23 WYM25 0.77 8.63E−03 2 11 WYM250.80 5.38E−03 2 22 WYM25 0.78 8.24E−03 2 24 WYM25 0.78 7.44E−03 2 19WYM25 0.77 9.23E−03 2 25 WYM25 0.74 1.50E−02 2 15 WYM25 0.78 8.19E−03 216 WYM25 0.80 5.33E−03 2 14 WYM25 0.78 8.22E−03 2 20 WYM25 0.79 6.72E−032 17 WYM25 0.78 8.25E−03 2 10 WYM25 0.78 7.39E−03 2 23 WYM26 0.775.81E−03 1 11 WYM26 0.74 9.07E−03 1 22 WYM26 0.79 3.90E−03 1 24 WYM260.77 5.38E−03 1 19 WYM26 0.93 4.41E−05 1 12 WYM26 0.76 6.30E−03 1 7WYM26 0.83 1.66E−03 1 5 WYM26 0.81 2.30E−03 1 25 WYM26 0.77 5.96E−03 115 WYM26 0.76 7.04E−03 1 3 WYM26 0.79 3.95E−03 1 16 WYM26 0.74 8.81E−031 14 WYM26 0.78 4.56E−03 1 20 WYM26 0.90 1.54E−04 1 13 WYM26 0.721.17E−02 1 17 WYM26 0.76 7.03E−03 1 8 WYM26 0.73 1.08E−02 1 10 WYM260.74 9.36E−03 1 2 WYM26 0.78 4.64E−03 1 23 WYM26 0.81 4.33E−03 2 11WYM26 0.82 3.76E−03 2 22 WYM26 0.75 1.19E−02 2 24 WYM26 0.81 4.75E−03 219 WYM26 0.79 6.55E−03 2 12 WYM26 0.71 2.08E−02 2 25 WYM26 0.88 8.81E−042 15 WYM26 0.74 1.46E−02 2 16 WYM26 0.85 1.77E−03 2 14 WYM26 0.787.67E−03 2 20 WYM26 0.88 8.82E−04 2 13 WYM26 0.77 9.90E−03 2 17 WYM260.83 2.91E−03 2 10 WYM26 0.72 2.00E−02 2 2 WYM26 0.78 7.81E−03 2 23WYM27 0.74 9.81E−03 1 11 WYM27 0.72 1.30E−02 1 19 WYM27 0.86 7.50E−04 112 WYM27 0.86 7.19E−04 1 7 WYM27 0.76 6.79E−03 1 15 WYM27 0.72 1.22E−021 14 WYM27 0.73 1.11E−02 1 20 WYM27 0.81 2.68E−03 1 13 WYM27 0.757.45E−03 1 17 WYM27 0.85 8.11E−04 1 8 WYM27 0.71 1.41E−02 1 10 WYM280.76 6.12E−03 1 11 WYM28 0.80 3.03E−03 1 22 WYM28 0.86 6.25E−04 1 24WYM28 0.86 6.84E−04 1 19 WYM28 0.81 2.33E−03 1 7 WYM28 0.87 5.80E−04 125 WYM28 0.80 3.18E−03 1 15 WYM28 0.88 4.10E−04 1 16 WYM28 0.85 8.82E−041 14 WYM28 0.85 9.63E−04 1 20 WYM28 0.82 2.15E−03 1 13 WYM28 0.831.56E−03 1 17 WYM28 0.78 5.04E−03 1 8 WYM28 0.77 5.62E−03 1 10 WYM280.80 3.41E−03 1 2 WYM28 0.87 4.38E−04 1 23 WYM29 0.78 8.03E−03 2 11WYM29 0.81 4.78E−03 2 22 WYM29 0.81 4.37E−03 2 24 WYM29 0.83 3.15E−03 219 WYM29 0.80 5.00E−03 2 7 WYM29 0.81 4.22E−03 2 25 WYM29 0.79 6.14E−032 15 WYM29 0.82 3.31E−03 2 16 WYM29 0.83 3.29E−03 2 14 WYM29 0.805.04E−03 2 20 WYM29 0.76 1.14E−02 2 13 WYM29 0.78 8.18E−03 2 8 WYM290.79 6.66E−03 2 10 WYM29 0.80 5.32E−03 2 2 WYM29 0.83 3.17E−03 2 23WYM30 0.73 1.08E−02 1 7 WYM30 0.71 1.49E−02 1 8 WYM31 0.82 1.97E−03 1 11WYM31 0.77 5.14E−03 1 22 WYM31 0.84 1.28E−03 1 24 WYM31 0.83 1.61E−03 119 WYM31 0.76 6.13E−03 1 12 WYM31 0.89 2.60E−04 1 7 WYM31 0.81 2.66E−031 25 WYM31 0.81 2.27E−03 1 15 WYM31 0.79 3.88E−03 1 16 WYM31 0.794.01E−03 1 14 WYM31 0.85 8.91E−04 1 20 WYM31 0.80 3.08E−03 1 13 WYM310.74 8.99E−03 1 17 WYM31 0.89 2.70E−04 1 8 WYM31 0.78 5.01E−03 1 10WYM31 0.83 1.62E−03 1 2 WYM31 0.82 2.13E−03 1 23 WYM31 0.75 1.22E−02 211 WYM31 0.71 2.08E−02 2 22 WYM31 0.77 9.72E−03 2 12 WYM31 0.85 1.94E−032 7 WYM31 0.74 1.44E−02 2 13 WYM31 0.83 2.83E−03 2 8 WYM31 0.74 1.46E−022 10 WYM32 0.86 6.81E−04 1 12 WYM32 0.81 2.75E−03 1 7 WYM32 0.784.92E−03 1 13 WYM32 0.71 1.44E−02 1 17 WYM32 0.80 3.44E−03 1 8 WYM320.74 1.39E−02 2 12 WYM32 0.72 1.93E−02 2 5 WYM33 0.80 3.20E−03 1 7 WYM330.78 4.22E−03 1 8 WYM33 0.70 2.40E−02 2 21 WYM34 0.73 1.04E−02 1 12WYM34 0.91 8.90E−05 1 7 WYM34 0.77 6.08E−03 1 15 WYM34 0.93 3.40E−05 1 8WYM34 0.80 3.03E−03 1 2 WYM35 0.83 1.52E−03 1 11 WYM35 0.85 9.90E−04 122 WYM35 0.89 2.81E−04 1 24 WYM35 0.89 2.81E−04 1 19 WYM35 0.88 3.57E−041 12 WYM35 0.83 1.42E−03 1 7 WYM35 0.88 3.89E−04 1 25 WYM35 0.812.36E−03 1 15 WYM35 0.88 3.03E−04 1 16 WYM35 0.86 7.69E−04 1 14 WYM350.88 3.46E−04 1 20 WYM35 0.92 5.89E−05 1 13 WYM35 0.78 4.70E−03 1 17WYM35 0.81 2.49E−03 1 8 WYM35 0.82 1.86E−03 1 10 WYM35 0.81 2.44E−03 1 2WYM35 0.89 2.23E−04 1 23 WYM99 0.73 1.65E−02 2 12 WYM99 0.71 2.08E−02 27 WYM99 0.76 1.07E−02 2 5 WYM99 0.72 1.90E−02 2 8 Table 41: Correlations(R) between the genes expression levels in various tissues and thephenotypic performance. “Corr. ID”—correlation set ID according to thecorrelated parameters Table above. “Exp. Set”—Expression set. “R” =Pearson correlation coefficient; “P” = p value.

Example 9 Production of Foxtail Millet Transcriptome and High ThroughputCorrelation Analysis Using 60K Foxtail Millet OligonucleotideMicro-Array

In order to produce a high throughput correlation analysis comparingbetween plant phenotype and gene expression level, the present inventorsutilized a foxtail millet oligonucleotide micro-array, produced byAgilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot)chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?1Page=50879]. Thearray oligonucleotide represents about 60K foxtail millet genes andtranscripts. In order to define correlations between the levels of RNAexpression and yield or vigor related parameters, various plantcharacteristics of 15 different foxtail millet accessions were analyzed.Among them, 11 accessions encompassing the observed variance wereselected for RNA expression analysis. The correlation between the RNAlevels and the characterized parameters was analyzed using Pearsoncorrelation test [Hypertext Transfer Protocol://World Wide Web (dot)davidmlane (dot) com/hyperstat/A34739 (dot) html].

Experimental Procedures

Analyzed Foxtail Millet Tissues—

three tissues at different developmental stages [leaf, flower, andstem], representing different plant characteristics, were sampled andRNA was extracted as described above. Each micro-array expressioninformation tissue type has received a Set ID as summarized in Table 42below.

TABLE 42 Foxtail millet transcriptome expression sets under normalconditions Expression Set Set ID flower: flowering stage 1 leaf:flowering stage 2 grain: grain filling stage: normal 4 leaf: grainfitting stage: normal 5 stem: grain filling stage: normal 6 Table 42:Provided are the foxtail millet transcriptome expression sets undernormal conditions

Foxtail Millet Yield Components and Vigor Related Parameters Assessment—

14 Foxtail millet accessions in 5 repetitive plots, in the field.Foxtail millet seeds were sown in soil and grown under normal conditionin the field. Plants were continuously phenotyped during the growthperiod and at harvest (Table 44-45, below). The image analysis systemincluded a personal desktop computer (Intel P4 3.0 GHz processor) and apublic domain program—ImageJ 1.37 (Java based image processing program,which was developed at the U.S. National Institutes of Health and freelyavailable on the internet [Hypertext Transfer Protocol://rsbweb (dot)nih (dot) gov/]. Next, analyzed data was saved to text files andprocessed using the JMP statistical analysis software (SAS institute).

The following parameters were collected using digital imaging system: Atthe end of the growing period the grains were separated from the Plant‘Head’ and the following parameters were measured and collected:

(i) Average Grain Area (cm²)—

A sample of ˜200 grains was weighted, photographed and images wereprocessed using the below described image processing system. The grainarea was measured from those images and was divided by the number ofgrains.

(ii) Average Grain Length and Width (cm)—

A sample of ˜200 grains was weighted, photographed and images wereprocessed using the below described image processing system. The sum ofgrain lengths and width (longest axis) was measured from those imagesand was divided by the number of grains.

At the end of the growing period 14 ‘Heads’ were photographed and imageswere processed using the below described image processing system.

(i) Head Average Area (cm²)

The ‘Head’ area was measured from those images and was divided by thenumber of ‘Heads’.

(ii) Head Average Length (mm)

The ‘Head’ length (longest axis) was measured from those images and wasdivided by the number of ‘Heads’.

The image processing system was used, which consists of a personaldesktop computer (Intel P4 3.0 GHz processor) and a public domainprogram—ImageJ 1.37. Java based image processing software, which wasdeveloped at the U.S. National Institutes of Health and is freelyavailable on the internet at Hypertext Transfer Protocol://rsbweb (dot)nih (dot) gov/. Images were captured in resolution of 10 Mega Pixels(3888×2592 pixels) and stored in a low compression JPEG (JointPhotographic Experts Group standard) format. Next, image processingoutput data for seed area and seed length was saved to text files andanalyzed using the JMP statistical analysis software (SAS institute).

Additional parameters were collected either by sampling 5 plants perplot or by measuring the parameter across all the plants within theplot.

Total Grain Weight (Gr.)—

At the end of the experiment (plant ‘Heads’) heads from plots werecollected, the heads were threshed and grains were weighted. Inaddition, the average grain weight per head was calculated by dividingthe total grain weight by number of total heads per plot (based onplot).

Head Weight and Head Number—

At the end of the experiment, heads were harvested from each plot andwere counted and weighted (kg.).

Biomass at Harvest—

At the end of the experiment the vegetative material from plots wasweighted.

Dry weight=total weight of the vegetative portion above ground(excluding roots) after drying at 70° C. in oven for 48 hours atharvest.

Total Dry Mater Per Plot—

Calculated as Vegetative portion above ground plus all the heads dryweight per plot.

Number (Num) Days to Anthesis—

Calculated as the number of days from sowing till 50% of the plotarrives at anthesis.

Maintenance of Performance Under Drought Conditions:

Represent ratio for the specified parameter of Drought condition resultsdivided by Normal conditions results (maintenance of phenotype underdrought in comparison to normal conditions).

Data parameters collected are summarized in Table 43, herein below

TABLE 43 Foxtail millet correlated parameters (vectors) Correlatedparameter with Correlation ID Biomass at harvest 1 Grain area 2 Grainlength 3 Grain width 4 Grains weight per Head (plot) 5 Head Area 6 Headlength 7 Heads num 8 Num days to Anthesis 9 Total Grains weight 10 Totaldry matter 11 Total heads weight 12 Table 43: Provided are the foxtailmillet collected parameters.

Experimental Results

14 different foxtail millet accessions were grown and characterized fordifferent parameters as described above. The average for each of themeasured parameter was calculated using the JMP software and values aresummarized in Tables 44-45 below. Subsequent correlation analysisbetween the various transcriptome sets and the average parameters wasconducted. Follow, results were integrated to the database.

TABLE 44 Measured parameters of correlation IDs in foxtail milletaccessions under normal conditions Line Correlation ID 1 2 3 4 5 6 7 12.14 3.99 3.17 3.58 3.60 3.06 4.04 2 0.03 0.04 0.03 0.03 0.03 0.03 0.033 0.24 0.24 0.25 0.25 0.26 0.25 0.23 4 0.17 0.19 0.17 0.16 0.16 0.170.16 5 3.40 7.29 1.49 1.30 1.57 0.69 2.10 6 37.83 57.87 19.59 17.1019.76 9.42 22.92 7 23.13 24.25 17.56 14.79 15.38 8.56 16.08 8 427.60149.20 867.00 1204.00 1146.40 2132.00 752.20 9 34.00 41.00 45.00 41.0041.00 30.00 38.00 10 1449.63 1067.88 1302.82 1567.20 1794.80 1476.111582.57 11 0.62 0.85 0.96 0.92 0.90 0.48 0.92 12 3.81 5.95 6.20 5.646.27 6.07 6.32 1 2.14 3.99 3.17 3.58 3.60 3.06 4.04 2 0.03 0.04 0.030.03 0.03 0.03 0.03 Table 44: Provided are the values of each of theparameters (as described above) measured in Foxtail millet accessions(line) under normal growth conditions. Growth conditions are specifiedin the experimental procedure section.

TABLE 45 Additional measured parameters of correlation IDs in foxtailmillet accessions under normal conditions Line Correlation ID 8 9 10 1112 13 14 1 1.15 3.20 3.90 3.58 3.68 2.94 1.48 2 0.02 0.03 0.02 0.04 0.030.04 0.03 3 0.20 0.22 0.20 0.26 0.25 0.27 0.24 4 0.15 0.18 0.16 0.180.17 0.18 0.16 5 3.34 11.46 7.17 4.35 2.26 0.44 1.31 6 40.89 45.29 49.3427.69 24.18 7.13 14.69 7 21.88 20.41 23.32 20.87 17.98 6.35 9.78 8394.20 186.60 131.80 434.20 646.40 2797.80 994.60 9 30.00 38.00 51.0044.00 51.00 31.00 27.00 10 1317.88 2131.60 937.93 1880.21 1427.121216.24 1296.69 11 0.45 0.59 1.00 0.91 1.03 0.62 0.46 12 2.82 7.25 5.246.58 5.85 5.62 2.73 1 1.15 3.20 3.90 3.58 3.68 2.94 1.48 2 0.02 0.030.02 0.04 0.03 0.04 0.03 Table 45: Provided are the values of each ofthe parameters (as described above) measured in Foxtail milletaccessions (line) under normal growth conditions. Growth conditions arespecified in the experimental procedure section.

TABLE 46 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance of maintenance of performance under drought conditionsacross foxtail millet varieties Gene Exp. Corr. Gene Exp. Corr. Name R Pvalue set Set ID Name R P value set Set ID WYM102 0.95 0.00 6 5 WYM1020.70 0.05 6 10 WYM102 0.83 0.01 6 6 WYM102 0.86 0.03 2 5 WYM102 0.710.11 2 10 WYM103 0.87 0.03 2 5 WYM103 0.80 0.06 2 7 WYM103 0.80 0.06 2 4WYM103 0.83 0.04 2 6 WYM36 0.71 0.01 1 7 WYM36 0.80 0.00 1 9 WYM36 0.740.01 4 12 WYM36 0.79 0.01 4 5 WYM36 0.92 0.00 4 10 WYM36 0.73 0.04 6 7WYM36 0.73 0.04 6 6 WYM36 0.74 0.10 2 5 WYM36 0.97 0.00 2 7 WYM36 0.860.03 2 4 WYM36 0.90 0.01 2 6 WYM36 0.74 0.01 3 11 WYM36 0.72 0.02 3 9WYM37 0.87 0.00 6 5 WYM37 0.91 0.00 6 10 WYM37 0.81 0.01 6 7 WYM37 0.940.00 6 6 WYM37 0.77 0.07 2 3 WYM37 0.86 0.03 2 8 WYM38 0.77 0.03 6 2WYM38 0.83 0.00 3 5 WYM40 0.78 0.01 4 12 WYM40 0.74 0.01 4 11 WYM40 0.850.00 4 9 WYM40 0.88 0.00 4 1 WYM40 0.71 0.05 6 5 WYM41 0.84 0.00 1 2WYM41 0.73 0.04 6 11 WYM41 0.76 0.08 2 5 WYM41 0.71 0.11 2 6 Table 46:Correlations (R) between the genes expression levels in various tissuesand the phenotypic performance. “Corr. ID”—correlation set ID accordingto the correlated parameters Table above. “Exp. Set”—Expression set. “R”= Pearson correlation coefficient; “P” = p value.

Example 10 Production of Soybean (Glycine Max) Transcriptome and HighThroughput Correlation Analysis with Yield Parameters Using 44K B.Soybean Oligonucleotide Micro-Arrays

In order to produce a high throughput correlation analysis, the presentinventors utilized a Soybean oligonucleotide micro-array, produced byAgilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot)chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?1Page=50879]. Thearray oligonucleotide represents about 42,000 Soybean genes andtranscripts. In order to define correlations between the levels of RNAexpression with yield components or plant architecture relatedparameters or plant vigor related parameters, various plantcharacteristics of 29 different Glycine max varieties were analyzed and12 varieties were further used for RNA expression analysis. Thecorrelation between the RNA levels and the characterized parameters wasanalyzed using Pearson correlation test.

Correlation of Glycine max Genes' Expression Levels with PhenotypicCharacteristics Across Ecotype

Experimental Procedures

29 Soybean varieties were grown in three repetitive plots, in field.Briefly, the growing protocol was as follows: Soybean seeds were sown insoil and grown under normal conditions until harvest. In order to definecorrelations between the levels of RNA expression with yield componentsor plant architecture related parameters or vigor related parameters, 12different Soybean varieties (out of 29 varieties) were analyzed and usedfor gene expression analyses. Analysis was performed at twopre-determined time periods: at pod set (when the soybean pods areformed) and at harvest time (when the soybean pods are ready forharvest, with mature seeds).

Analyzed Soybean Tissues

In order to define correlations between the levels of RNA expressionwith yield components or plant architecture related parameters or vigorrelated parameters, 12 different Soybean varieties (out of 29 varieties)were analyzed and used for gene expression analyses as described above.Analysis was performed at two pre-determined time periods: at pod set(when the soybean pods are formed) and at harvest time (when the soybeanpods are ready for harvest, with mature seeds). Each micro-arrayexpression information tissue type has received a Set ID as summarizedin Table 47 below.

TABLE 47 Soybean transcriptome expression sets Expression Set Set IDApical meristem; before flowering 1 Leaf; before flowering 2 Leaf;flowering 3 Leaf; pod setting 4 Root; before flowering 5 Root: flowering6 Root: pod setting 7 Stem: before flowering 8 Stern; pod setting 9Young flowers: flowering 10 Pod; pod setting 11 Table 47. Provided arethe soybean transcriptome expression sets

RNA Extraction—

All 12 selected Soybean varieties were sample per treatment. Planttissues [leaf, root, Stem, Pod, apical meristem, Flower buds] growingunder normal conditions were sampled and RNA was extracted at the notedstages (e.g., before flowering, at flowering, at pod setting) asdescribed above.

The collected data parameters were as follows:

Main Branch Base Diameter [Mm] at Pod Set—

the diameter of the base of the main branch (based diameter) average ofthree plants per plot.

Fresh Weight [gr./Plant] at Pod Set—

total weight of the vegetative portion above ground (excluding roots)before drying at pod set, average of three plants per plot.

Dry Weight [gr./Plant] at Pod Set—

total weight of the vegetative portion above ground (excluding roots)after drying at 70° C. in oven for 48 hours at pod set, average of threeplants per plot.

Total Number of Nodes with Pods on Lateral Branches [Value/Plant]—

counting of nodes which contain pods in lateral branches at pod set,average of three plants per plot.

Number of Lateral Branches at Pod Set [Value/Plant]—

counting number of lateral branches at pod set, average of three plantsper plot.

Total Weight of Lateral Branches at Pod Set [gr./Plant]—

weight of all lateral branches at pod set, average of three plants perplot.

Total Weight of Pods on Main Stem at Pod Set [gr./Plant]—

weight of all pods on main stem at pod set, average of three plants perplot.

Total Number of Nodes on Main Stem [Value/Plant]—

count of number of nodes on main stem starting from first node aboveground, average of three plants per plot.

Total Number of Pods with 1 Seed on Lateral Branches at Pod Set[Value/Plant]—

count of the number of pods containing 1 seed in all lateral branches atpod set, average of three plants per plot.

Total Number of Pods with 2 Seeds on Lateral Branches at Pod Set[Value/Plant]—

count of the number of pods containing 2 seeds in all lateral branchesat pod set, average of three plants per plot.

Total Number of Pods with 3 Seeds on Lateral Branches at Pod Set[Value/Plant]—

count of the number of pods containing 3 seeds in all lateral branchesat pod set, average of three plants per plot.

Total Number of Pods with 4 Seeds on Lateral Branches at Pod Set[Value/Plant]—

count of the number of pods containing 4 seeds in all lateral branchesat pod set, average of three plants per plot.

Total Number of Pods with 1 Seed on Main Stem at Pod Set [Value/Plant]—

count of the number of pods containing 1 seed in main stem at pod set,average of three plants per plot.

Total Number of Pods with 2 Seeds on Main Stem at Pod Set [Value/Plant]—

count of the number of pods containing 2 seeds in main stem at pod set,average of three plants per plot.

Total Number of Pods with 3 Seeds on Main Stem at Pod Set [Value/Plant]—

count of the number of pods containing 3 seeds in main stem at pod set,average of three plants per plot.

Total Number of Pods with 4 Seeds on Main Stem at Pod Set [Value/Plant]—

count of the number of pods containing 4 seeds in main stem at pod set,average of three plants per plot.

Total Number of Seeds Per Plant at Pod Set [Value/Plant]—

count of number of seeds in lateral branches and main stem at pod set,average of three plants per plot.

Total Number of Seeds on Lateral Branches at Pod Set [Value/Plant]—

count of total number of seeds on lateral branches at pod set, averageof three plants per plot.

Total Number of Seeds on Main Stem at Pod Set [Value/Plant]—

count of total number of seeds on main stem at pod set, average of threeplants per plot.

Plant Height at Pod Set [cm/Plant]—

total length from above ground till the tip of the main stem at pod set,average of three plants per plot.

Plant Height at Harvest [cm/Plant]—

total length from above ground till the tip of the main stem at harvest,average of three plants per plot.

Total Weight of Pods on Lateral Branches at Pod Set [gr./Plant]—

weight of all pods on lateral branches at pod set, average of threeplants per plot.

Ratio of the Number of Pods Per Node on Main Stem at Pod Set—

calculated in formula XVII, average of three plants per plot.Total number of pods on main stem/Total number of nodes on main stem,average of three plants per plot.  Formula XVII

Ratio of Total Number of Seeds in Main Stem to Number of Seeds onLateral Branches—

calculated in Formula XVIII, average of three plants per plot.Total number of seeds on main stem at pod set/Total number of seeds onlateral branches at pod set.  Formula XVIII

Total Weight of Pods Per Plant at Pod Set [gr./Plant]—

weight of all pods on lateral branches and main stem at pod set, averageof three plants per plot.

Days Till 50% Flowering [Days]—

number of days till 50% flowering for each plot.

Days Till 100% Flowering [Days]—

number of days till 100% flowering for each plot.

Maturity [Days]—

measure as 95% of the pods in a plot have ripened (turned 100% brown).Delayed leaf drop and green stems are not considered in assigningmaturity. Tests are observed 3 days per week, every other day, formaturity. The maturity date is the date that 95% of the pods havereached final color. Maturity is expressed in days after August 31[according to the accepted definition of maturity in USA. Descriptorlist for SOYBEAN, Hypertext Transfer Protocol://World Wide Web (dot)ars-grin (dot) gov/cgi-bin/npgs/html/desclist (dot) pl?51].

Seed Quality [Ranked 1-5]—

measure at harvest; a visual estimate based on several hundred seeds.Parameter is rated according to the following scores considering theamount and degree of wrinkling, defective coat (cracks), greenishness,and moldy or other pigment. Rating is 1-very good, 2-good, 3-fair,4-poor, 5-very poor.

Lodging [Ranked 1-5]—

is rated at maturity per plot according to the following scores: 1-mostplants in a plot are erected; 2-all plants leaning slightly or a fewplants down; 3-all plants leaning moderately, or 25%-50% down; 4-allplants leaning considerably, or 50%-80% down; 5-most plants down. Note:intermediate score such as 1.5 are acceptable.

Seed Size [gr.]—

weight of 1000 seeds per plot normalized to 13% moisture, measure atharvest.

Total Weight of Seeds Per Plant [gr./Plant]—

calculated at harvest (per 2 inner rows of a trimmed plot) as weight ingrams of cleaned seeds adjusted to 13% moisture and divided by the totalnumber of plants in two inner rows of a trimmed plot.

Yield at Harvest [Bushels/Hectare]—

calculated at harvest (per 2 inner rows of a trimmed plot) as weight ingrams of cleaned seeds, adjusted to 13% moisture, and then expressed asbushels per acre.

Average Lateral Branch Seeds Per Pod [Number]—

Calculate Num of Seeds on lateral branches—at pod set and divide by theNumber of Total number of pods with seeds on lateral branches—at podset.

Average Main Stem Seeds Per Pod [Number]—

Calculate Total Number of Seeds on main stem at pod set and divide bythe Number of Total number of pods with seeds on main stem at podsetting.

Main Stem Average Internode Length [cm]—

Calculate Plant height at pod set and divide by the Total number ofnodes on main stem at pod setting.

Total Num of Pods with Seeds on Main Stem [Number]—

count all pods containing seeds on the main stem at pod setting.

Total Num of Pods with Seeds on Lateral Branches [Number]—

count all pods containing seeds on the lateral branches at pod setting.

Total Number of Pods Per Plant at Pod Set [Number]—

count pods on main stem and lateral branches at pod setting.

Data parameters collected are summarized in Table 48, herein below

TABLE 48 Correlation Correlated parameter with ID 100 percent flowering1  50 percent flowering 2 Base diameter at pod set 3 DW at pod set 4Lodging 5 Maturity 6 Num of lateral branches 7 Num of pods with 1 seedon main stem at pod set 8 Num of pods with 2 seed on main stem 9 Num ofpods with 3 seed on main stem 10 Num of pods with 4 seed on main stem 11Plant height at harvest 12 Plant height at pod set 13 Ratio number ofpods per node on main stem 14 Ratio number of seeds per main stem toseeds 15 per 1 Seed quality 16 Seed size 17 Total Number of Seeds onlateral branches 18 Total Number of Seeds on main stem at pod set 19Total no of pods with 1 seed on lateral branch 20 Total no of pods with2 seed on lateral branch 21 Total no of pods with 3 seed on lateralbranch 22 Total no of pods with 4 seed on lateral branch 23 Total numberof nodes on main stem 24 Total number of nodes with pods on lateralbranch 25 Total number of seeds per plant 26 Total weight of lateralbranches at pod set 27 Total weight of pods on lateral branches 28 Totalweight of pods on main stem at pod set 29 Total weight of pods per plant30 Total weight of seeds per plant 31 fresh weight at pod set 32 yieldat harvest 33 Table 48: Provided are the soybean correlated parameters.“DW” = dry weight;

Experimental Results

Twelve different Soybean varieties were grown and characterized for 33parameters as specified above. The average for each of the measuredparameters was calculated using the JMP software and values aresummarized in Tables 49-50 below. Subsequent correlation analysisbetween the various transcriptome expression sets and the averageparameters was conducted. Results were then integrated to the database.

TABLE 49 Measured parameters in Soybean varieties (lines 1-6) LineCorrelation ID Line-1 Line-2 Line-3 Line-4 Line-5 Line-6 1 67.33 71.6767.67 67.33 60 74 2 61 65.33 60.67 61 54.67 68.33 3 8.333 9.544 9.6788.111 8.822 10.12 4 53.67 50.33 38 46.17 60.83 55.67 5 1.667 1.833 1.1671.667 2.667 2.833 6 24 43.67 30.33 30.33 38.33 40 7 9 8.667 9.111 9.8897.667 17.56 8 1.111 4.375 1.444 1.444 4.556 1.667 9 16.89 16.25 13.2216.89 27 8.111 10 29.56 1.75 19.78 22.33 11.67 22.78 11 0 0 0.111 0.1110 0.444 12 96.67 76.67 67.5 75.83 74.17 76.67 13 86.78 69.56 62.44 70.8969.44 63.89 14 2.874 1.377 2.132 2.256 2.6 1.87 15 0.893 0.896 0.8690.891 2.316 0.365 16 2.333 3.5 3 2.167 2.833 2 17 89 219.3 93 86 191.371.33 18 150.9 55.89 134 160.4 75.44 324.6 19 123.6 43.89 87.67 102.793.56 88 20 1.556 3 1.778 1.778 5.667 5.625 21 17 18.75 26.44 32.3321.56 33.5 22 38.44 2 26.44 31.33 8.889 82 23 0 0 0 0 0 1.5 24 16.5616.78 16.11 18.11 16.78 17.11 25 23 16 23.11 33 15.22 45.25 26 274.499.78 221.7 263.1 169 412.5 27 67.78 63.78 64.89 74.89 54 167.2 28 2614.89 20.11 20.11 21.11 30.25 29 22.11 14.33 16 15 33.78 9 30 48.1129.22 36.11 35.11 54.89 38.88 31 15.09 10.5 17.23 16.51 12.06 10.25 32170.9 198.2 152.6 163.9 224.7 265 33 47.57 43.77 50.37 56.3 44 40.33Table 49: Provided are the values of each of the parameters (asdescribed above) measured in soybean accessions (line) under normalgrowth conditions. Growth conditions are specified in the experimentalprocedure section.

TABLE 50 Measured parameters in Soybean varieties (lines 7-12) LineCorrelation ID Line-7 Line-8 Line-9 Line-10 Line-11 Line-12 1 73 72.3368.67 73.67 68 70.67 2 66.5 65.67 62.33 67.67 61.67 64.33 3 8.456 8.0898.256 7.733 8.156 7.889 4 48 52 44.17 52.67 56 47.5 5 2.667 2.5 1.8333.5 3.333 1.5 6 41 38.33 31 39 27.33 32.67 7 11.67 12.11 8 9.111 6.77810 8 4 4.333 2.111 1.889 3.444 1.222 9 21.33 17.67 20.33 16.11 28.1116.56 10 11.11 28.22 24.11 36.44 39.67 32.33 11 0 0.556 0 3.889 0 0 12101.7 98.33 75.83 116.7 76.67 71.67 13 89.78 82.11 70.56 101.7 79.5667.22 14 1.98 2.712 2.777 2.754 3.7 2.836 15 3.9 0.783 1.183 1.984 1.0330.832 16 3.5 2.5 2.167 2.333 2.167 2.167 17 88 75 80.67 75.67 76.3377.33 18 46.88 176.2 143 105.4 184.3 187.3 19 80 126.6 115.1 159 178.7131.3 20 2.875 3 1.25 2.667 1.778 3 21 8.5 22.78 21.75 10.67 23.78 25.6722 9 42.11 32.75 25.67 45 44.33 23 0 0.333 0 1.111 0 0 24 18.78 18.8916.78 21.11 19.33 20.78 25 8.25 25.44 21.88 16.33 22.56 24.22 26 136302.8 260.5 264.4 363 318.7 27 45.44 83.22 64.33 52 76.89 67 28 4.12520.11 17 9.222 28.11 22.56 29 9.033 16 15.89 14.56 30.44 18 30 14.2536.11 32.75 23.78 58.56 40.56 31 7.297 11.38 15.68 10.83 12.98 15.16 32160.7 196.3 155.3 178.1 204.4 164.2 33 34.23 44.27 53.67 42.47 43.6 52.2Table 50: Provided are the values of each of the parameters (asdescribed above) measured in soybean accessions (line) under normalgrowth conditions. Growth conditions are specified in the experimentalprocedure section.

TABLE 51 Correlation between the expression level of selected genes ofsome embodiments of the invention in various tissues and the phenotypicperformance under normal conditions across soybean varieties P Exp.Corr. Gene P Exp. Corr. Gene Name R value set Set ID Name R value setSet ID WYM110 0.91 1.95E−03 9 31 WYM110 0.95 2.96E−04 9 33 WYM84 0.731.62E−02 7 32 WYM84 0.93 9.24E−05 7 3 WYM84 0.76 1.10E−02 8 31 WYM840.76 1.07E−02 8 33 WYM84 0.72 4.46E−02 9 10 WYM84 0.84 8.79E−03 9 31WYM84 0.82 1.32E−02 9 33 WYM84 0.84 9.00E−03 9 22 WYM84 0.86 6.02E−03 918 WYM84 0.89 3.37E−03 9 21 WYM84 0.82 1.35E−02 9 30 WYM84 0.79 2.00E−029 25 WYM84 0.92 1.13E−03 9 28 WYM84 0.91 1.93E−03 9 26 WYM84 0.754.97E−03 4 9 WYM85 0.87 5.03E−03 9 31 WYM85 0.75 3.21E−02 9 33 WYM850.70 5.24E−02 9 29 WYM85 0.72 8.08E−03 4 9 WYM85 0.85 4.80E−04 1 27WYM85 0.72 8.05E−03 1 25 WYM85 0.71 1.01E−02 1 3 WYM86 0.74 1.52E−02 731 WYM86 0.70 2.39E−02 8 31 WYM86 0.70 2.40E−02 8 33 WYM86 0.71 4.87E−029 31 WYM86 0.80 1.90E−03 4 20 WYM87 0.75 1.28E−02 7 20 WYM87 0.731.73E−02 5 30 WYM87 0.79 2.03E−02 9 31 WYM87 0.82 1.25E−02 9 33 Table51: Correlations (R) between the genes expression levels in varioustissues and the phenotypic performance. “Corr. ID”—correlation set IDaccording to the correlated parameters Table above. “Exp.Set”—Expression set. “R” = Pearson correlation coefficient; “P” = pvalue.

Example 11 Identification of Genes which can be Used to Increase Yieldand Other Agricultural Advantageous Traits

Overall, 99 genes (SEQ ID NOs: 1-219 for polynucleotides and SEQ ID NOs:220-366 for polypeptides) were identified to have a major impact onplant yield, growth rate, vigor, biomass, growth rate, oil content,abiotic stress tolerance, nitrogen use efficiency, water use efficiencyand fertilizer use efficiency when expression thereof is increased inplants. The identified genes, their curated polynucleotide andpolypeptide sequences, as well as their updated sequences according toGenBank database are summarized in Table 52, herein below.

TABLE 52 Identified genes for increasing yield, growth rate, vigor,biomass, oil content, abiotic stress tolerance, nitrogen use efficiency,water use efficiency and fertilizer use efficiency of a plant Polyp.Polyn. SEQ SEQ ID Gene Name Cluster Name Organism ID NO: NO: LAB278_H0maize|10v1|AW054293 maize 1 220 LNU74_H109 maize|10v1|AI621531 maize 2221 LAM208_H4 sorghum|09v1|SB01G032070 sorghum 3 222 LYM490_H1maize|10v1|W21761 maize 4 223 WYM1 barley|l0v2|AJ228941 barley 5 224WYM2 barley|10v2|AJ436276 barley 6 225 WYM3 barley|10v2|AJ460753 barley7 226 WYM4 barley|10v2|AV833173 barley 8 227 WYM7 barley|10v2|BE194594barley 9 228 WYM8 barley|10v2|BE195883 barley 10 229 WYM9barley|10v2|BE214668 barley 11 230 WYM11 barley|10v2|BE412454 barley 12231 WYM12 barley|10v2|BE420686 barley 13 232 WYM13 barley|10v2|BF623573barley 14 233 WYM15 barley|10v2|BI946842 barley 15 234 WYM16barley|10v2|BI947216 barley 16 235 WYM17 barley|10v2|BI947796 barley 17236 WYM18 barley|10v2|BJ452833 barley 18 237 WYM19 barley|10v2|CB870239barley 19 238 WYM20 barley|10v2|DN158111 barley 20 239 WYM21brachypodium|09v1| brachypodium 21 240 BRADI3G52760 WYM22brachypodium|09v1|DV475781 brachypodium 22 241 WYM23brachypodium|09v1|DV476706 brachypodium 23 242 WYM24brachypodium|09v1|DV485069 brachypodium 24 243 WYM25brachypodium|09v1|GT758373 brachypodium 25 244 WYM26brachypodium|09v1|GT759637 brachypodium 26 245 WYM27brachypodium|09v1|GT764687 brachypodium 27 246 WYM28brachypodium|09v1|GT765082 brachypodium 28 247 WYM29brachypodium|09v1|GT770393 brachypodium 29 248 WYM30brachypodium|09v1|GT775433 brachypodium 30 249 WYM31brachypodium|09v1|GT780903 brachypodium 31 250 WYM32brachypodium|09v1|GT784287 brachypodium 32 251 WYM33brachypodium|09v1|GT791163 brachypodium 33 252 WYM34brachypodium|09v1|GT847927 brachypodium 34 253 WYM35 brachypodium|09v1|brachypodium 35 254 SRR031795S0012454 WYM36foxtail_millet|10v2|SICRP015958 foxtail_millet 36 255 WYM37foxtail_millet|10v2|SICRP017191 foxtail_millet 37 256 WYM38foxtail_millet|11v1| foxtail_millet 38 257 FOXTAILXMILLETX10V2XFXTRMSLX00055016D1XT1 WYM40 foxtail_millet|11v1| foxtail_millet 39 258FOXTAILXMILLETX10V2XFXT RMSLX01384364D1XT1 WYM41 foxtail_millet|11v1|foxtail_millet 40 259 FOXTAILXMILLETX10V2XFXT SLX00803709D1XT1 WYM42maize|10v1|AA054812 maize 41 260 WYM43 maize|10v1|AA979730 maize 42 261WYM44 maize|10v1|AA979748 maize 43 262 WYM46 maize|10v1|AI372300 maize44 263 WYM47 maize|10v1|AI586615 maize 45 264 WYM48 maize|10v1|AI600444maize 46 265 WYM51 maize|10v1|AI649490 maize 47 266 WYM52maize|10v1|AI665357 maize 48 267 WYM55 maize|10v1|AI920337 maize 49 268WYM56 maize|10v1|AI920394 maize 50 269 WYM57 maize|10v1|AI974918 maize51 270 WYM58 maize|10v1|AW267325 maize 52 271 WYM59 maize|10v1|AW506641maize 53 272 WYM60 maize|10v1|BE055910 maize 54 273 WYM61maize|10v1|BG355067 maize 55 274 WYM62 maize|10v1|BG458626 maize 56 275WYM63 maize|10v1|BI245239 maize 57 276 WYM64 maize|10v1|BQ621148 maize58 277 WYM65 maize|10v1|CD948252 maize 59 278 WYM66 maize|10v1|T26937maize 60 279 WYM67 maize|10v1|T70625 maize 61 280 WYM69maize|10v1|W59834 maize 62 281 WYM70 rice|gb170|OS03G48080 rice 63 282WYM71 rice|gb170|OS07G44290 rice 64 283 WYM72 sorghum|09v1|SB01G030550sorghum 65 284 WYM74 sorghum|09v1|SB02G002690 sorghum 66 285 WYM76sorghum|09v1|SB03G037080 sorghum 67 286 WYM77 sorghum|09v1|SB04G005000sorghum 68 287 WYM79 sorghum|09v1|SB06G001610 sorghum 69 288 WYM80sorghum|09v1|SB06G032750 sorghum 70 289 WYM81 sorghum|09v1|SB09G030000sorghum 71 290 WYM83 sorghum|09v1|SB10G029670 sorghum 72 291 WYM84soybean|11v1|CD405767 soybean 73 292 WYM85 soybean|11v1| soybean 74 293GLYMA02G41040 WYM86 soybean|11v1| soybean 75 294 GLYMA05G25910 WYM87soybean|11v1| soybean 76 295 GLYMA07G08240 WYM89 wheat|10v2|BE401050wheat 77 296 WYM90 wheat|10v2|BE401466 wheat 78 297 WYM91wheat|10v2|BE418556 wheat 79 298 WYM92 wheat|10v2|BE423194 wheat 80 299WYM93 wheat|10v2|BE497501 wheat 81 300 WYM94 wheat|10v2|BE604122 wheat82 301 WYM95 wheat|10v2|CA656649 wheat 83 302 WYM96 wheat|10v2|CA660726wheat 84 303 WYM98 maize|10v1|AI964515 maize 85 304 WYM99brachypodium|09v1|DV472468 brachypodium 86 305 WYM100brachypodium|09v1|DV475214 brachypodium 87 306 WYM101brachypodium|09v1|GT774209 brachypodium 88 307 WYM102foxtail_millet|10v2| foxtail_millet 89 308 SICRP028266 WYM103foxtail_millet|11v1| foxtail_millet 90 309 FOXTAILXMILLETX10V2XFXTRMSLX06595039D1XT1 WYM104 maize|10v1|AI734660 maize 91 310 WYM105maize|10v1|AW000637 maize 92 311 WYM106 maize|10v1|BG320875 maize 93 312WYM107 maize|10v1|CF034815 maize 94 313 WYM108 maize|10v1|MZEPPGM maize95 314 WYM109 rice|gb170|OS08G02210 rice 96 315 WYM110soybean|11v1|GLYMA06G12470 soybean 97 316 WYM112 wheat|10v2|BE399157wheat 98 317 WYM113 wheat|10v2|BF474853 wheat 99 318 WYM3barley|10v2|AJ460753 barley 100 319 WYM7 barley|10v2|BE194594 barley 101320 WYM12 barley|10v2|BE420686 barley 102 321 WYM17 barley|10v2|BI947796barley 103 322 WYM18 barley|10v2|BJ452833 barley 104 323 WYM19barley|10v2|CB870239 barley 105 324 WYM20 barley|10v2|DN158111 barley106 325 WYM21 brachypodium|09v1| brachypodium 107 240 BRADI3G52760 WYM26brachypodium|09v1|GT759637 brachypodium 108 245 WYM27brachypodium|09v1|GT764687 brachypodium 109 246 WYM28brachypodium|09v1|GT765082 brachypodium 110 247 WYM29brachypodium|09v1|GT770393 brachypodium 111 248 WYM34brachypodium|09v1|GT847927 brachypodium 112 253 WYM35 brachypodium|09v1|brachypodium 113 326 SRR031795S0012454 WYM37 foxtail_millet|10v2|foxtail_millet 114 256 SICRP017191 WYM40 foxtail_millet|11v1|foxtail_millet 115 258 FOXTAILXMILLETX10V2XFXT RMSLX01384364D1XT1 WYM41foxtail_millet|11v1| foxtail_millet 116 259 FOXTAILXMILLETX10V2XFXTSLX00803709D1XT1 WYM56 maize|10v1|AI920394 maize 117 327 WYM85soybean|11v1| soybean 118 328 GLYMA02G41040 WYM87 soybean|11v1| soybean119 295 GLYMA07G08240 WYM89 wheat|10v2|BE401050 wheat 120 329 WYM90wheat|10v2|BE401466 wheat 121 330 WYM102 foxtail_millet|10v2|foxtail_millet 122 331 SICRP08266 WYM104 maize|10v1|AI734660 maize 123310 WYM106 maize|10v1|BG320875 maize 124 332 LAB278_H0maize|10v1|AW054293 maize 125 333 LNU74_H109 maize|10v1|AI621531 maize126 221 LYM208_H4 sorghum|09v1|SB01G032070 sorghum 127 334 LYM490_H1maize|10v1|W21761 maize 128 335 WYM1 barley|10v2|AJ228941 barley 129 224WYM2 barley|10v2|AJ436276 barley 130 225 WYM3 barley|10v2|AJ460753barley 131 336 WYM4 barley|10v2|AV833173 barley 132 337 WYM7barley|10v2|BE194594 barley 133 338 WYM8 barley|10v2|BE195883 barley 134229 WYM9 barley|10v2|BE214668 barley 135 339 WYM11 barley|10v2|BE412454barley 136 231 WYM12 barley|10v2|BE420686 barley 137 340 WYM13barley|10v2|BF623573 barley 138 233 WYM15 barley|10v2|BI946842 barley139 234 WYM16 barley|10v2|BI947216 barley 140 235 WYM17barley|10v2|BI947796 barley 141 341 WYM18 barley|10v2|BJ452833 barley142 342 WYM20 barley|10v2|DN158111 barley 143 343 WYM21brachypodium|09v1| brachypodium 144 240 BRADI3G52760 WYM22brachypodium|09v1|DV475781 brachypodium 145 241 WYM23brachypodium|09v1|DV476706 brachypodium 146 344 WYM24brachypodium|09v1|DV485069 brachypodium 147 345 WYM25brachypodium|09v1|GT758373 brachypodium 148 244 WYM26brachypodium|09v1|GT759637 brachypodium 149 245 WYM27brachypodium|09v1|GT764687 brachypodium 150 246 WYM28brachypodium|09v1|GT765082 brachypodium 151 247 WYM29brachypodium|09v1|GT770393 brachypodium 152 248 WYM30brachypodium|09v1|GT775433 brachypodium 153 249 WYM31brachypodium|09v1|GT780903 brachypodium 154 346 WYM32brachypodium|09v1|GT784287 brachypodium 155 251 WYM33brachypodium|09v1|GT791163 brachypodium 156 252 WYM34brachypodium|09v1|GT847927 brachypodium 157 347 WYM35 brachypodium|09v1|brachypodium 158 348 SRR031795S0012454 WYM36 foxtail_millet|10v2|foxtail_millet 159 255 SICRP015958 WYM37 foxtail_millet|10v2|foxtail_millet 160 256 SICRP017191 WYM38 foxtail_millet|11v1|foxtail_millet 161 257 FOXTAILXMILLETX10V2XFXT RMSLX00055016D1XT1 WYM40foxtail_millet|11v1| foxtail_millet 162 349 FOXTAILXMILLETX10V2XFXTRMSLX01384364D1XT1 WYM42 maize|10v1|AA054812 maize 163 260 WYM43maize|10v1|AA979730 maize 164 350 WYM44 maize|10v1|AA979748 maize 165262 WYM46 maize|10v1|AI372300 maize 166 263 WYM47 maize|10v1|AI586615maize 167 264 WYM48 maize|10v1|AI600444 maize 168 351 WYM51maize|10v1|AI649490 maize 169 266 WYM52 maize|10v1|AI665357 maize 170267 WYM55 maize|10v1|AI920337 maize 171 268 WYM56 maize|10v1|AI920394maize 172 269 WYM57 maize|10v1|AI974918 maize 173 352 WYM58maize|10v1|AW267325 maize 174 353 WYM59 maize|10v1|AW506641 maize 175272 WYM60 maize|10v1|BE055910 maize 176 273 WYM61 maize|10v1|BG355067maize 177 354 WYM62 maize|10v1|BG458626 maize 178 355 WYM63maize|10v1|BI245239 maize 179 276 WYM64 maize|10v1|BQ621148 maize 180277 WYM65 maize|10v1|CD948252 maize 181 278 WYM66 maize|10v1|T26937maize 182 279 WYM67 maize|10v1|T70625 maize 183 280 WYM69maize|10v1|W59834 maize 184 281 WYM70 rice|gb170|OS03G48080 rice 185 282WYM71 rice|gb170|OS07G44290 rice 186 283 WYM72 sorghum|09v1|SB01G030550sorghum 187 356 WYM74 sorghum|09v1|SB02G002690 sorghum 188 285 WYM76sorghum|09v1|SB03G037080 sorghum 189 286 WYM77 sorghum|09v1|SB04G005000sorghum 190 357 WYM79 sorghum|09v1|SB06G001610 sorghum 191 288 WYM80sorghum|09v1|SB06G032750 sorghum 192 358 WYM81 sorghum|09v1|SB09G030000sorghum 193 290 WYM83 sorghum|09v1|SB10G029670 sorghum 194 291 WYM84soybean|11v1|CD405767 soybean 195 292 WYM85 soybean|11v1|GLYMA02G41040soybean 196 293 WYM86 soybean|11v1|GLYMA05G25910 soybean 197 294 WYM87soybean|11v1|GLYMA07G08240 soybean 198 359 WYM90 wheat|10v2|BE401466wheat 199 360 WYM91 wheat|10v2|BE418556 wheat 200 361 WYM92wheat|10v2|BE423194 wheat 201 299 WYM93 wheat|10v2|BE497501 wheat 202300 WYM94 wheat|10v2|BE604122 wheat 203 301 WYM95 wheat|10v2|CA656649wheat 204 362 WYM96 wheat|10v2|CA660726 wheat 205 363 WYM98maize|10v1|AI964515 maize 206 304 WYM99 brachypodium|09v1|DV472468brachypodium 207 364 WYM100 brachypodium|09v1|DV475214 brachypodium 208306 WYM101 brachypodium|09v1|GT774209 brachypodium 209 365 WYM103foxtail_millet|11v1| foxtail_millet 210 309 FOXTAILXMILLETX10V2XFXTRMSLX06595039D1XT1 WYM104 maize|10v1|AI734660 maize 211 310 WYM105maize|10v1|AW000637 maize 212 311 WYM106 maize|10v1|BG320875 maize 213312 WYM107 maize|10v1|CF034815 maize 214 313 WYM108 maize|10v1|MZEPPGMmaize 215 314 WYM109 rice|gb170|OS08G02210 rice 216 315 WYM110soybean|11v1|GLYMA06G12470 soybean 217 316 WYM112 wheat|10v2|BE399157wheat 218 366 WYM113 wheat|10v2|BF474853 wheat 219 318 LYM90barley|gb157.3|AV927104_CT1 barley 9688 9701 LYM91barley|gb157.3|BE060518_CT1 barley 9689 9702 LYM320barley|gb157SOLEXA|BE421502 barley 9690 9703 LYM332barley|gb157SOLEXA|BI947101 barley 9691 9704 LYM350 maize|gb170|AI612450maize 9697 9705 LAB259 rice|gb170|OS09G31482 rice 9693 9708 LYM90barley|gb157.3|AV927104_T1 barley 9694 9701 LYM90barley|gb157.3|AV927104_T1 barley 9695 9701 LYM91barley|gb157.3|BE060518_T1 barley 9696 9702 LYM320barley|gb157SOLEXA|BE421502 barley 9697 9706 LYM332barley|gb157SOLEXA|BI947101 barley 9698 9707 LYM350 maize|gb170|AI612450maize 9699 9705 LAB259 rice|gb170|OS09G31482 rice 9700 9708 Table 52:Provided are the identified genes (core genes SEQ ID NOs: 1-99, corepolypeptides: SEQ ID NOs: 220-318), their annotation, organism andpolynucleotide and polypeptide sequence identifiers. Also provided arethe polynucleotides variants SEQ ID NOs: 100-124 and their encodedpolypeptides and the cloned polynucleotides SEQ ID NOs: 125-219 andtheir encoded polypeptides. “polyn.” = polynucleotide; “polyp.” =polypeptide.

Example 12 Identification of Homologous Sequences that Increase Yield,Fiber Yield, Fiber Quality, Growth Rate, Biomass, Oil Content, Vigor,ABST, and/or NUE of a Plant

The concepts of orthology and paralogy have recently been applied tofunctional characterizations and classifications on the scale ofwhole-genome comparisons. Orthologs and paralogs constitute two majortypes of homologs: The first evolved from a common ancestor byspecialization, and the latter are related by duplication events. It isassumed that paralogs arising from ancient duplication events are likelyto have diverged in function while true orthologs are more likely toretain identical function over evolutionary time.

To further investigate and identify putative orthologs of the genesaffecting plant yield, oil yield, oil content, seed yield, growth rate,vigor, biomass, abiotic stress tolerance, and fertilizer use efficiency(FUE) genes and/or nitrogen use efficiency, all sequences were alignedusing the BLAST (Basic Local Alignment Search Tool). Sequencessufficiently similar were tentatively grouped. These putative orthologswere further organized under a Phylogram—a branching diagram (tree)assumed to be a representation of the evolutionary relationships amongthe biological taxa. Putative ortholog groups were analyzed as to theiragreement with the phylogram and in cases of disagreements theseortholog groups were broken accordingly.

Expression data was analyzed and the EST libraries were classified usinga fixed vocabulary of custom terms such as developmental stages (e.g.,genes showing similar expression profile through development with upregulation at specific stage, such as at the seed filling stage) and/orplant organ (e.g., genes showing similar expression profile across theirorgans with up regulation at specific organs such as seed). Theannotations from all the ESTs clustered to a gene were analyzedstatistically by comparing their frequency in the cluster versus theirabundance in the database, allowing the construction of a numeric andgraphic expression profile of that gene, which is termed “digitalexpression”. The rationale of using these two complementary methods withmethods of phenotypic association studies of QTLs, SNPs and phenotypeexpression correlation is based on the assumption that true orthologsare likely to retain identical function over evolutionary time. Thesemethods provide different sets of indications on function similaritiesbetween two homologous genes, similarities in the sequencelevel-identical amino acids in the protein domains and similarity inexpression profiles.

The search and identification of homologous genes involves the screeningof sequence information available, for example, in public databases suchas the DNA Database of Japan (DDBJ), GenBank, and the European MolecularBiology Laboratory Nucleic Acid Sequence Database (EMBL) or versionsthereof or the MIPS database. A number of different search algorithmshave been developed, including but not limited to the suite of programsreferred to as BLAST programs. There are five implementations of BLAST,three designed for nucleotide sequence queries (BLASTN. BLASTX, andTBLASTX) and two designed for protein sequence queries (BLASTP andTBLASTN) (Coulson, Trends in Biotechnology: 76-80, 1994: Birren et al.,Genome Analysis. I: 543, 1997). Such methods involve alignment andcomparison of sequences. The BLAST algorithm calculates percent sequenceidentity and performs a statistical analysis of the similarity betweenthe two sequences. The software for performing BLAST analysis ispublicly available through the National Centre for BiotechnologyInformation. Other such software or algorithms are GAP. BESTFIT, FASTAand TFASTA. GAP uses the algorithm of Needleman and Wunsch (J. Mol.Biol. 48: 443-453, 1970) to find the alignment of two complete sequencesthat maximizes the number of matches and minimizes the number of gaps.

The homologous genes may belong to the same gene family. The analysis ofa gene family may be carried out using sequence similarity analysis. Toperform this analysis one may use standard programs for multiplealignments e.g. Clustal W. A neighbour-joining tree of the proteinshomologous to the genes in this invention may be used to provide anoverview of structural and ancestral relationships. Sequence identitymay be calculated using an alignment program as described above. It isexpected that other plants will carry a similar functional gene(ortholog) or a family of similar genes and those genes will provide thesame preferred phenotype as the genes presented here. Advantageously,these family members may be useful in the methods of the invention.Example of other plants are included here but not limited to, barley(Hordeum vulgare), Arabidopsis (Arabidopsis thaliana), maize (Zea mays),cotton (Gossypium), Oilseed rape (Brassica napus), Rice (Oryza sativa),Sugar cane (Saccharum officinarum). Sorghum (Sorghum bicolor), Soybean(Glycine max), Sunflower (Helianthus annuus). Tomato (Lycopersiconesculentum). Wheat (Triticum aestivum).

The above-mentioned analyses for sequence homology can be carried out ona full-length sequence, but may also be based on a comparison of certainregions such as conserved domains. The identification of such domains,would also be well within the realm of the person skilled in the art andwould involve, for example, a computer readable format of the nucleicacids of the present invention, the use of alignment software programsand the use of publicly available information on protein domains,conserved motifs and boxes. This information is available in the PRODOM(Hypertext Transfer Protocol://World Wide Web (dot) biochem (dot) ucl(dot) ac (dot) uk/bsm/dbbrowser/protocol/prodomqry (dot) html), PIR(Hypertext Transfer Protocol://pir (dot) Georgetown (dot) edu/) or Pfam(Hypertext Transfer Protocol://World Wide Web (dot) sanger (dot) ac(dot) uk/Software/Pfam/) database. Sequence analysis programs designedfor motif searching may be used for identification of fragments, regionsand conserved domains as mentioned above. Preferred computer programsinclude, but are not limited to, MEME, SIGNALSCAN, and GENESCAN.

A person skilled in the art may use the homologous sequences providedherein to find similar sequences in other species and other organisms.Homologues of a protein encompass peptides, oligopeptides, polypeptides,proteins and enzymes having amino acid substitutions, deletions and/orinsertions relative to the unmodified protein in question and havingsimilar biological and functional activity as the unmodified proteinfrom which they are derived. To produce such homologues, amino acids ofthe protein may be replaced by other amino acids having similarproperties (conservative changes, such as similar hydrophobicity,hydrophilicity, antigenicity, propensity to form or break a-helicalstructures or 3-sheet structures). Conservative substitution tables arewell known in the art (see for example Creighton (1984) Proteins. W.H.Freeman and Company). Homologues of a nucleic acid encompass nucleicacids having nucleotide substitutions, deletions and/or insertionsrelative to the unmodified nucleic acid in question and having similarbiological and functional activity as the unmodified nucleic acid fromwhich they are derived.

Polynucleotides and polypeptides with significant homology to theidentified genes described in Table 52 (Example 11 above) wereidentified from the databases using BLAST software with the Blastp andtBlastn algorithms as filters for the first stage, and the needle(EMBOSS package) or Frame+ algorithm alignment for the second stage.Local identity (Blast alignments) was defined with a very permissivecutoff—60% Identity on a span of 60% of the sequences lengths because itis used only as a filter for the global alignment stage. The defaultfiltering of the Blast package was not utilized (by setting theparameter “-F F”).

In the second stage, homologs were defined based on a global identity ofat least 80% to the core gene polypeptide sequence. Two distinct formsfor finding the optimal global alignment for protein or nucleotidesequences were used in this application:

1. Between two proteins (following the blastp filter):

EMBOSS-6.0.1 Needleman-Wunsch algorithm with the following modifiedparameters: gapopen=8 gapextend=2. The rest of the parameters wereunchanged from the default options described hereinabove.

2. Between a protein sequence and a nucleotide sequence (following thetblastn filter):

GenCore 6.0 OneModel application utilizing the Frame+ algorithm with thefollowing parameters: model=frame+_p2n.model mode=qglobal-q=protein.sequence -db=nucleotide.sequence. The rest of the parametersare unchanged from the default options described hereinabove.

The query polypeptide sequences were SEQ ID NOs: 220-366 and 9701-9708(which are encoded by the polynucleotides SEQ ID NOs:1-219 and9688-9693, shown in Table 52 above) and the identified orthologous andhomologous sequences having at least 80% global sequence identity areprovided in Table 53, below. These homologous genes are expected toincrease plant yield, seed yield, oil yield, oil content, growth rate,fiber yield, fiber quality, biomass, vigor, ABST and/or NUE of a plant.

Lengthy table referenced here US11242538-20220208-T00001 Please refer tothe end of the specification for access instructions.

The output of the functional genomics approach described herein is a setof genes highly predicted to improve yield and/or other agronomicimportant traits such as growth rate, vigor, oil content, fiber yieldand/or quality, biomass, abiotic stress tolerance, nitrogen useefficiency, water use efficiency and fertilizer use efficiency of aplant by increasing their expression. Although each gene is predicted tohave its own impact, modifying the mode of expression of more than onegene is expected to provide an additive or synergistic effect on theplant yield and/or other agronomic important yields performance.Altering the expression of each gene described here alone or set ofgenes together increases the overall yield and/or other agronomicimportant traits, hence expects to increase agricultural productivity.

Example 13 Gene Cloning and Generation of Binary Vectors for PlantExpression

To validate their role in improving plant yield, oil content, seedyield, biomass, growth rate, fiber yield, fiber quality. ABST. NUEand/or vigor, selected genes were over-expressed in plants, as follows.

Cloning Strategy

Selected genes from those listed in Examples 1-12 hereinabove werecloned into binary vectors for the generation of transgenic plants. Forcloning, the full-length open reading frame (ORF) was first identified.In case of ORF-EST clusters and in some cases already published mRNAsequences were analyzed to identify the entire open reading frame bycomparing the results of several translation algorithms to knownproteins from other plant species. To clone the full-length cDNAs,reverse transcription (RT) followed by polymerase chain reaction (PCR;RT-PCR) was performed on total RNA extracted from leaves, flowers,siliques or other plant tissues, growing under normal and differenttreated conditions. Total RNA was extracted as described in “GENERALEXPERIMENTAL AND BIOINFORMATICS METHODS” above. Production of cDNA andPCR amplification was performed using standard protocols describedelsewhere (Sambrook J., E. F. Fritsch, and T. Maniatis, 1989. MolecularCloning. A Laboratory Manual., 2nd Ed. Cold Spring Harbor LaboratoryPress, New York.), which are well known to those skilled in the art. PCRproducts were purified using PCR purification kit (Qiagen). In casewhere the entire coding sequence was not found, RACE kit from Invitrogen(RACE=Rapid Amplification of cDNA Ends) was used to access the full cDNAtranscript of the gene from the RNA samples described above. RACEproducts were cloned into high copy vector followed by sequencing ordirectly sequenced.

The information from the RACE procedure was used for cloning of the fulllength ORF of the corresponding genes.

In case genomic DNA was cloned, the genes are amplified by direct PCR ongenomic DNA extracted from leaf tissue using the DNAeasy kit (QiagenCat. No. 69104).

Usually, 2 sets of primers were synthesized for the amplification ofeach gene from a cDNA or a genomic sequence; an external set of primersand an internal set (nested PCR primers). When needed (e.g., when thefirst PCR reaction does not result in a satisfactory product forsequencing), an additional primer (or two) of the nested PCR primers isused.

To facilitate cloning of the cDNAs/genomic sequences, an 8-12 bpextension was added to the 5′ of each primer. The primer extensionincludes an endonuclease restriction site. The restriction sites wereselected using two parameters: (a). The site does not exist in the cDNAsequence; and (b). The restriction sites in the forward and reverseprimers were designed such that the digested cDNA was inserted in thesense formation into the binary vector utilized for transformation.

PCR products were digested with the restriction endonucleases (NewEngland BioLabs Inc) according to the sites designed in the primers.Each digested PCR product was inserted into a high copy vector pUC19(New England BioLabs Inc], or into plasmids originating from thisvector. In some cases the undigested PCR product was inserted intopCR-Blunt II-TOPO (Invitrogen) or directly into the binary vector.

Sequencing of the amplified PCR products was performed, using ABI 377sequencer (Amersham Biosciences Inc). In some cases, after confirmingthe sequences of the cloned genes, the cloned cDNA was introduced into amodified pGI binary vector containing the At6669 promoter via digestionwith appropriate restriction endonucleases. The digested products andthe linearized plasmid vector were ligated using T4 DNA ligase enzyme(Roche, Switzerland).

High copy plasmids containing the cloned genes were digested with therestriction endonucleases (New England BioLabs Inc) according to thesites designed in the primers and cloned into binary vectors.

Several DNA sequences of the selected genes were synthesized by acommercial supplier GeneArt [Hypertext Transfer Protocol://World WideWeb (dot) geneart (dot) com/]. Synthetic DNA was designed in silico.Suitable restriction enzymes sites were added to the cloned sequences atthe 5′ end and at the 3′ end to enable later cloning into the pQFNc orother required binary vector downstream of the At6669 promoter (SEQ IDNO: 9405).

Binary Vectors Used for Cloning:

The plasmid pPI was constructed by inserting a synthetic poly-(A) signalsequence, originating from pGL3 basic plasmid vector (Promega, Acc NoU47295; bp 4658-4811) into the HindIII restriction site of the binaryvector pBI101.3 (Clontech. Acc. No. U12640). pGI (pBXYN) was similar topPI, but the original gene in the backbone, the GUS gene, was replacedby the GUS-Intron gene followed by the NOS terminator (SEQ ID NO: 9419)(Vancanneyt. G, et al MGG 220, 245-50, 1990), pGI was used in the pastto clone the polynucleotide sequences, initially under the control of35S promoter [Odell, J T, et al. Nature 313, 810-812 (28 Feb. 1985); SEQID NO:9403].

The modified pGI vectors [pQXNc (FIG. 8); or pQFN (FIG. 2), pQFNc (FIG.2) or pQYN_6669 (FIG. 1)] were modified versions of the pGI vector inwhich the cassette was inverted between the left and right borders sothe gene and its corresponding promoter were close to the right borderand the NPTII gene was close to the left border.

At6669, the Arabidopsis thaliana promoter sequence (SEQ ID NO: 9405) wasinserted in the modified pGI binary vector, upstream to the clonedgenes, followed by DNA ligation and binary plasmid extraction frompositive E. coli colonies, as described above.

Colonies were analyzed by PCR using the primers covering the insertwhich are designed to span the introduced promoter and gene. Positiveplasmids were identified, isolated and sequenced.

Selected genes cloned by the present inventors are provided in Table 54below.

TABLE 54 Genes cloned in high copy number plasmids Polyn. Polyp. Primersused SEQ SEQ Gene Name High copy plasmid Organism SEQ ID NOs: ID NO: IDNO: LAB259 pKSJ_LAB259 rice 9700 9708 LYM320 pUC19c_LYM320 barley 96979706 LYM332 pUC19c_LYM332 barley 9698 9707 LYM350_GA pMA-RQ_LYM350_GAGeneArt 9699 9705 LYM90 pGXN_LYM90 barley 9695 9701 LYM91 pGXN_LYM91barley 9696 9702 WYM113 pMA-RQ_WYM113_GA GeneArt 219 318 WYM112pUC19c_WYM112 wheat 9649, 9434, 9434, 9434 218 366 WYM109 pUC19c_WYM109rice 9514, 9432, 9432, 9432 216 315 WYM108 pUC19c_WYM108 maize 9513,9431, 9431, 9431 215 314 WYM107 pUC19c_WYM107 maize 9648, 9592, 9592,9592 214 313 WYM106 pUC19_WYM106 maize 9647, 9591, 9591, 9591 213 312WYM105 pUC19c_WYM105 maize 9510, 9428, 9428, 9428 212 311 WYM104pUC19c_WYM104 maize 9646, 9590, 9590, 9590 211 310 WYM103 pUC19c_WYM103foxtail_millet 9645, 9589, 9589, 9589 210 309 WYM101 pUC19c_WYM101brachypodium 9644, 9588, 9588, 9588 209 365 WYM100 pQFNc_WYM100brachypodium 9643, 9587, 9587, 9587 208 306 WYM99 pUC19c_WYM99brachypodium 9583, 9640, 9640, 9640 207 364 WYM98 pUC19_WYM98 maize9687, 9639, 9639, 9639 206 304 WYM96 pUC19c_WYM96 wheat 9581, 9638,9638, 9638 205 363 WYM95 pUC19d_WYM95 wheat 9580, 9637, 9637, 9637 204362 WYM94 pUC19c_WYM94 wheat 9686, 9636, 9636, 9636 203 301 WYM93pUC19c_WYM93 wheat 9578, 9635, 9635, 9635 202 300 WYM92 pUC19c_WYM92wheat 9685, 9634, 9634, 9634 201 299 WYM91 pUC19c_WYM91 wheat 9684,9633, 9633, 9633 200 361 WYM90 pUC19c_WYM90 wheat 9575, 9493, 9493, 9493199 360 WYM87 pUC19c_WYM87 soybean 9373, 9491, 9491, 9491 198 359 WYM86pUC19c_WYM86 soybean 9372, 9490, 9490, 9490 197 294 WYM85 pUC19c_WYM85soybean 9682, 9632, 9632, 9632 196 293 WYM84 pUC19c_WYM84 soybean 9681,9631, 9631, 9631 195 292 WYM83 pUC19c_WYM83 sorghum 9369, 9487, 9487,9487 194 291 WYM81 pUC19c_WYM81 sorghum 9568, 9486, 9486, 9486 193 290WYM80 pUC19c_WYM80 sorghum 9680, 9630, 9630, 9630 192 358 WYM79pUC19c_WYM79 sorghum 9679, 9629, 9629, 9629 191 288 WYM77 pUC19c_WYM77sorghum 9678, 9628, 9628, 9628 190 357 WYM76 pUC19_WYM76 sorghum 9564,9627, 9627, 9627 189 286 WYM74 pUC19c_WYM74 sorghum 9677, 9626, 9626,9626 188 285 WYM72 pQFNc_WYM72 sorghum 9676, 9623, 9625, 9625 187 356WYM71 pUC19c_WYM71 rice 9562, 9480, 9480, 9480 186 283 WYM70 pQFNc_WYM70rice 9675, 9624, 9624, 9624 185 282 WYM69 pUC19c_WYM69 maize 9560, 9478,9478, 9478 184 281 WYM67 pUC19c_WYM67 maize 9674, 9477, 9477, 9477 183280 WYM66 pUC19c_WYM66 maize 9673, 9622, 9622, 9622 182 279 WYM65pUC19c_WYM65 maize 9672, 9621, 9621, 9621 181 278 WYM64 pMA-RQ_WYM64_GA180 277 WYM63 pUC19c_WYM63 maize 9671, 9620, 9620, 9620 179 276 WYM62pUC19c_WYM62 maize 9556, 9474, 9474, 9474 178 355 WYM61 pUC19c_WYM61maize 9670, 9619, 9619, 9619 177 354 WYM60 pQFNc_WYM60 maize 9669, 9618,9618, 9618 176 273 WYM59 pUC19c_WYM59 maize 9668, 9617, 9617, 9617 175272 WYM58 pUC19c_WYM58 maize 9667, 9616, 9616, 9616 174 353 WYM57pUC19c_WYM57 maize 9666, 9615, 9615, 9615 173 352 WYM56 pMA-RQ_WYM56_GA172 269 WYM55 pUC19c_WYM55 maize 9665, 9614, 9614, 9614 171 268 WYM52pUC19c_WYM52 maize 9549, 9613, 9613, 9613 170 267 WYM51 pUC19c_WYM51maize 9548, 9466, 9466, 9466 169 266 WYM48 pUC19c_WYM48 maize 9547,9465, 9465, 9465 168 351 WYM47 pUC19c_WYM47 maize 9664, 9612, 9612, 9612167 264 WYM46 pUC19c_WYM46 maize 9663, 9463, 9463, 9463 166 263 WYM44pUC19c_WYM44 maize 9662, 9611, 9611, 9611 165 262 WYM43 pUC19c_WYM43maize 9544, 9610, 9610, 9610 164 350 WYM42 pUC19c_WYM42 maize 9661,9609, 9609, 9609 163 260 WYM40 TopoB_WYM40 foxtail_millet 9542, 9460,9460, 9460 162 349 WYM38 pUC19c_WYM38 foxtail_millet 9540, 9608, 9608,9608 161 257 WYM37 pUC19c_WYM37 foxtail_millet 9660, 9607, 9607, 9607160 256 WYM36 pUC19c_WYM36 foxtail_millet 9659, 9606, 9606, 9606 159 255WYM35 pUC19c_WYM35 brachypodium 9658, 9605, 9605, 9605 158 348 WYM34pQFNc_WYM34 brachypodium 9657, 9601, 9604, 9604 157 347 WYM33pUC19c_WYM33 brachypodium 9535, 9453, 9453, 9453 156 252 WYM32pUC19d_WYM32 brachypodium 9534, 9603, 9603, 9603 155 251 WYM31pUC19c_WYM31 brachypodium 9656, 9602, 9602, 9602 154 346 WYM30pUC19c_WYM30 brachypodium 9655, 9601, 9601, 9601 153 249 WYM29pUC19c_WYM29 brachypodium 9530, 9448, 9448, 9448 152 248 WYM28pUC19c_WYM28 brachypodium 9529, 9600, 9600, 9600 151 247 WYM27pUC19c_WYM27 brachypodium 9528, 9446, 9446, 9446 150 246 WYM26pUC19c_WYM26 brachypodium 9527, 9599, 9599, 9599 149 245 WYM25pUC19c_WYM25 brachypodium 9526, 9444, 9444, 9444 148 244 WYM24pUC19c_WYM24 brachypodium 9525, 9443, 9443, 9443 147 345 WYM23pUC19c_WYM23 brachypodium 9654, 9598, 9598, 9598 146 344 WYM22pUC19c_WYM22 brachypodium 9524, 9597, 9597, 9597 145 241 WYM21pUC19c_WYM21 brachypodium 9653, 9441, 9441, 9441 144 240 WYM20pQFNc_WYM20 barley 9522, 9440, 9440, 9440 143 343 WYM18 pUC19c_WYM18barley 9521, 9439, 9439, 9439 142 342 WYM17 pUC19c_WYM17 barley 9520,9595, 9595, 9595 141 341 WYM16 pQFNc_WYM16 barley 9651, 9594, 9594, 9594140 235 WYM15 pUC19c_WYM15 barley 9518, 9436, 9436, 9436 139 234 WYM13pUC19c_WYM13 barley 9650, 9593, 9593, 9593 138 233 WYM12 pUC19c_WYM12barley 9517, 9435, 9435, 9435 137 340 WYM11 pUC19c_WYM11 barley 9515,9433, 9433, 9433 136 231 WYM9 pUC19c_WYM9 barley 9683, 9492, 9492, 9492135 339 WYM8 pQFNc_WYM8 barley 9566, 9484, 9484, 9484 134 229 WYM7pUC19_WYM7 barley 9561, 9623, 9623, 9623 133 338 WYM4 pUC19c_WYM4 barley9541, 9459, 9459, 9459 132 337 WYM3 pUC19c_WYM3 barley 9531, 9449, 9449,9449 131 336 WYM2 pUC19c_WYM2 barley 9652, 9596, 9596, 9596 130 225 WYM1pUC19c_WYM1 barley 9505, 9586, 9586, 9586 129 224 WYM110 pMA-T_WYM110_GA217 316 LYM490_H1 pUC19c_LYM490H1 maize 9504, 9422, 9422, 9422 128 335LYM208_H4 pUC19c_LYM208H4 sorghum 9642, 9585, 9585, 9585 127 334LNU74_H109 pUC19c_LNU74H109 maize 9641, 9584, 9584, 9584 126 221LAB278_H0 pUC19_LAB278H0 maize 9502, 9420, 9420, 9420 125 333 Table 54.“Polyn.” - Polynucleotide; “Polyp.” - polypeptide. For cloning of eachgene at least 2 primers were used: Forward (Fwd) or Reverse (Rev). Insome cases, 4 primers were used: External forward (EF), External reverse(ER), nested forward (NF) or nested reverse (NR). The sequences of theprimers used for cloning the genes are provided in the sequence listing.The genes were cloned from the same organism as identified in the listof genes provided in Table 52 above, except for the genes that weresynthetically produced by GeneArt.

Example 14 Transforming Agrobacterium Tumefaciens Cells with BinaryVectors Harboring Putative Genes

Each of the binary vectors described in Example 13 above were used totransform Agrobacterium cells. An additional binary construct was usedas negative control containing empty vector carrying At6669 promoter andthe selection marker.

For transformation in Arabidopsis plants, the binary vectors wereintroduced to Agrobacterium tumefaciens GV301, GV303 or LB4404 competentcells (about 10⁹ cells/mL) by electroporation.

For transformation into Brachypodium, the binary vectors were introducedinto Agrobacterium tumefaciens AGLI.

The electroporation was performed using a MicroPulser electroporator(Biorad), 0.2 cm cuvettes (Biorad) and EC-2 electroporation program(Biorad). The treated cells were cultured in LB liquid medium at 28° C.for 3 hours, then plated over LB agar supplemented with gentamycin (50mg/L; for Agrobacterium strains GV301) or streptomycin (300 mg/L; forAgrobacterium strain LB4404) and kanamycin (50 mg/L) at 28° C. for 48hours. Agrobacterium colonies, which were developed on the selectivemedia, were analyzed by PCR using the primers which were designed tospan the inserted sequence in the pPI plasmid. The resulting PCRproducts were isolated and sequenced as described in Example 13 above,to verify that the correct nucleotide sequences were properly introducedto the Agrobacterium cells.

Example 15 Producing Transgenic Arabidopsis Plants Expressing SelectedGenes According to Some Embodiments of the Invention

Materials and Experimental Methods

Plant Transformation—

The Arabidopsis thaliana var Columbia (T₀ plants) were transformedaccording to the Floral Dip procedure [Clough S J, Bent A F. (1998)Floral dip: a simplified method for Agrobacterium-mediatedtransformation of Arabidopsis thaliana. Plant J. 16(6): 735-43; andDesfeux C, Clough S J. Bent A F. (2000) Female reproductive tissues arethe primary targets of Agrobacterium-mediated transformation by theArabidopsis floral-dip method. Plant Physiol. 123(3): 895-904] withminor modifications. Briefly, Arabidopsis thaliana Columbia (Col0) T₀plants were sown in 250 ml pots filled with wet peat-based growth mix.The pots were covered with aluminum foil and a plastic dome, kept at 4°C. for 3-4 days, then uncovered and incubated in a growth chamber at18-24° C. under 16/8 hours light/dark cycles. The T₀ plants were readyfor transformation six days before anthesis.

Single colonies of Agrobacterium carrying the binary vectors harboringthe yield genes were cultured in LB medium supplemented with kanamycin(50 mg/L) and gentamycin (50 mg/L). The cultures were incubated at 28°C. for 48 hours under vigorous shaking and centrifuged at 4000 rpm for 5minutes. The pellets comprising Agrobacterium cells were resuspended ina transformation medium which contained half-strength (2.15 g/L)Murashige-Skoog (Duchefa); 0.044 μM benzylamino purine (Sigma); 112 μg/LB5 Gambourg vitamins (Sigma): 5% sucrose; and 0.2 ml/L Silwet L-77 (OSISpecialists, CT) in double-distilled water, at pH of 5.7.

Transformation of T₀ plants was performed by inverting each plant intoan Agrobacterium suspension such that the above ground plant tissue wassubmerged for 3-5 seconds. Each inoculated T₀ plant was immediatelyplaced in a plastic tray, then covered with clear plastic dome tomaintain humidity and was kept in the dark at room temperature for 18hours to facilitate infection and transformation. Transformed(transgenic) plants were then uncovered and transferred to a greenhousefor recovery and maturation. The transgenic T₀ plants were grown in thegreenhouse for 3-5 weeks until siliques were brown and dry, then seedswere harvested from plants and kept at room temperature until sowing.

For generating T₁ and T₂ transgenic plants harboring the genes, seedscollected from transgenic T₀ plants were surface-sterilized by soakingin 70% ethanol for 1 minute, followed by soaking in 5% sodiumhypochlorite and 0.05% triton for 5 minutes. The surface-sterilizedseeds were thoroughly washed in sterile distilled water then placed onculture plates containing half-strength Murashig-Skoog (Duchefa); 2%sucrose; 0.8% plant agar; 50 mM kanamycin; and 200 mM carbenicylin(Duchefa). The culture plates were incubated at 4° C. for 48 hours thentransferred to a growth room at 25° C. for an additional week ofincubation. Vital T₁ Arabidopsis plants were transferred to a freshculture plates for another week of incubation. Following incubation theT₁ plants were removed from culture plates and planted in growth mixcontained in 250 ml pots. The transgenic plants were allowed to grow ina greenhouse to maturity. Seeds harvested from T₁ plants were culturedand grown to maturity as T2 plants under the same conditions as used forculturing and growing the T₁ plants.

Example 16 Transformation of Brachypodium Distachyon Plants with thePolynucleotides of the Invention

Similar to the Arabidopsis model plant, Brachypodium distachyon hasseveral features that recommend it as a model plant for functionalgenomic studies, especially in the grasses. Traits that make it an idealmodel include its small genome (˜355 Mbp), small physical stature, ashort lifecycle, and few growth requirements. Brachypodium is related tothe major cereal grain species but is understood to be more closelyrelated to the Triticeae (wheat, barley) than to the other cereals.Brachypodium, with its polyploidy accessions, can serve as an idealmodel for these grains (whose genomics size and complexity is a majorbarrier to biotechnological improvement).

Brachypodium distachyon embryogenic calli were transformed using theprocedure described by Vogel and Hill (2008) (High-efficiencyAgrobacterium-mediated transformation of Brachypodium distachyon inbredline Bd21-3. Plant Cell Rep 27:471-478) and by Vain et al (2008)(Agrobacterium-mediated transformation of the temperate grassBrachypodium distachyon (genotypeBd21) for T-DNA insertionalmutagenesis. Plant Biotechnology J 6: 236-245), each of which is fullyincorporated herein by reference, with some minor modifications.

Briefly, compact embryogenic calli were derived from immature embryos ofBrachypodium distachyon accession Bd21-3, an inbred diploid line.Appropriate immature bell-shaped embryos and of size ˜0.3 mm, wereplated onto CIM medium+2, 4-Dichlorophenoxyacetic acid (2.5 mg/l, SIGMA.Catalogue number: D7299)+CuSO₄.5H₂O (0.6 mg/l. Sigma, Catalogue number:C3036). One liter (1 L) of CIM medium was prepared by adding thefollowing components to a final volume of 1 liter water (H₂O):LS+vitamins 4.4 grams (Duchefa, Catalogue number: L0230); Sucrose 30grams (Duchefa, Catalogue number: S0809); Phytagel 2 grams (SIGMA.Catalogue number: P8169). After two weeks in culture, the embryogeniccalli were fragmented into 4 to 6 pieces each, and plated on the sameCIM medium with 2, 4-Dichlorophenoxyacetic acid and CuSO₄.5H₂O. Twoweeks later, the calli were fragmented and plated again (no more than 25calli per plate). By 4 weeks in culture the calli were ready forinfection with Agrobacterium.

Single colonies of Agrobacterium carrying the binary vectors harboringthe yield genes were cultured over a plate of MGL medium containing 50mg/l (milligrams per liter) kanamicin, 50 mg/l carbenicillin andacetosyringone 200 μM (micromolar) final. One liter (1 L) of MGL mediumwas prepared by adding the following components to a final volume of 1liter water (H₂O): Yeast extract 2.5 grams (HIMEDIA. Catalogue number:RM027), Triptone 5 grams (Duchefa. Catalogue number: T1332). NaCl 5grams (BioLab. Catalogue number: 19030591), MgSO₄×7H2O 204 milligrams(SIGMA, Catalogue number: M1880), D-Manitol 5 grams (Duchefa, Cataloguenumber: D0803). KH₂PO₄ 250 milligrams (Duchefa. Catalogue number:P0574). Glutamic Acid 1.2 grams (Duchefa. Catalogue number: G0707).After 24 hours at 28° C. the Agrobacterium layer which was scraped fromplate was resuspended into 40 ml of MS medium (containing acetosyringone200 μM), and placed on a shaker at 220 rpm for 45 minutes in a 28° C.incubator. Then, the Agrobacterium suspension was diluted to O.D. 1.0with MS medium. Ten ml of the diluted Agrobacterium suspension weredispensed onto each of plates containing the embryonic calli andincubated for 5 minutes inoculation in a laminar flow hood at room temp.Then, the suspension was completely removed from the plates, callipieces were handpicked onto a filter in a dry Petri dish, where theywere dried by desiccation for several minutes. The blotted calli werethen plated (25 pieces per plate) onto a filter wetted with 750 μl of MSmedium, where they were co-cultivation with the Agrobacterium for 2 daysat 25° C. in the dark.

Selection of transformed calli was done on plates containing 30 ml ofCIM medium+2,4-Dichlorophenoxyacetic (2.5 mg/l) CuSO₄.5H₂O (0.0.6mg/l)+Ticarcillin disodium (400 mg/l)+Hygromycin Sulfate (40 mg/l)medium, that were cultured for 2 weeks in the dark. The surviving calliwere then transferred to fresh medium where they were cultured foradditional 2 weeks. Four weeks after transformation, the calli weretransferred onto Shoot Induction Medium (SIM) medium (Linsmaier andSkoog Physiol. Plantarum, 18:100, 1965, which is fully incorporatedherein by reference)+6-Benzylaminopurin riboside (1 mg/l)+IAA (0.25mg/l)+CuSO₄ (0.6 mg/l)+ascorbic acid (20 mg/l)+Tic (200 mg/l)+HM (40mg/l), where shoots of T₀ plants start to regenerate during 2 weeks at25° C. under a 16 hour light/8 hour dark photoperiod. Regenerated shootswere transferred to maturation medium consist of Nitsch [Nitsch saltsand vitamins 2.18 g/l+sucrose 15 g/l pH 5.8+phytagel 0.2%]+α-NaphthaleneAcetic Acid (2 mg/l)+Indole-3-Acetic Acid (1 mg/l) medium, where theyregenerate roots in 2 to 3 weeks.

Regenerated transgenic T₀ plants were grown in the greenhouse for ˜3months until seed maturation and spikelet drying. Seeds were harvestedfrom plants and kept at 10° C. until sowing. For the generation of T₁and T₂ transgenic plants that harbor the transformed genes,surface-sterilized seeds were collected from transgenic T₀ plants andplaced in trays with sowing mix containing 0.3 ml/L BASTA selection with60 mg/L DL-Phoshpinothricin active ingredient. The sowing trays wereincubated at 4° C. for 72 hours and then transferred to a growth room at25° C. for an additional 10-12 days of incubation. Vital T₁ brachypodiumplants were transferred to growth mix in validation plots that wereplaced in the greenhouse, where they grow up to maturity. Seedsharvested from T₁ plants were germinated and grown to maturity as T2plants under the same conditions as described for T₁ plants.

Example 17 Transformation of Triticum Aestivum L Plants with thePolynucleotides of the Invention

Triticum aestivum embryogenic calli were transformed using the proceduredescribed in U.S. Pat. No. 7,238,862, which is fully incorporated hereinby reference in its entirety. Briefly, immature embryos of wheat cvBobwhite were isolated from the immature caryopsis (wheat spikelets)12-15 days after pollination, and cultured on M7 medium for 4-6 days.The embryos without embryogenic callus were selected for Agrobacteriuminoculation.

Agrobacterium is grown on solid medium at 28° C. for 3 days and then at23° C. for 1 day. The Agrobacterium was then directly collected on thesolid medium, diluted with 1/10 CM4C medium [MS basal salts withvitamins, sucrose, agar and supplemented with specific growthregulators; provided by BIOWORLD, Dublin. Ohio 43017. USA, Catalogue No.30630121-1 (759995)] and used for inoculation. Explants were incubatedwith the washed and resuspended Agrobacterium cell suspension. Theinoculation was generally performed at a temperature of 24° C.-26° C.,from about 1 minute to about 3 hours. After the inoculation period, theinoculated immature embryos were placed in plates with filter paperWhatman No. 1 wetted with 200 μl sterile water 20-50 embryos X4/plate.Plates were parafilmed and incubated in the dark, 24-26° C. for 2-3days. After such 3-day co-cultivation, the Agrobacterium-infectedprecultured immature embryos (PCIE) and embryogenic calli weretransferred to CM4C medium supplemented with 500 mg/L carbenicillin andcultured for about seven days for selection and plant regeneration. This“delay” medium can also contain glyphosate (0.02 mM). The infectedprecultured immature embryos explants formed embryogenic callus on thismedium.

The explants were then transferred to CM4C selection medium with 2 mMglyphosate and 500 mg/L carbenicillin for one week in the dark. All thecalli were transferred to MMS0.2C medium (1×MS salts and Vitamins, 1.95g/L MES, 0.2 mg/L 2,4-D, and 40 g/L maltose, pH 5.6, solidified by 2 g/LGelrite; after autoclaving, adding 100 mg/L ascorbic acid) supplementedwith 0.1 mM glyphosate and 250 mg/L carbenicillin (first regenerationmedium) for an additional two weeks of selection with lightingconditions of about 80 μE. Green spots or shoots formed at the end ofthis culture period. All the embryogenic calli were transferred to thesecond regeneration medium MMS0C supplemented with 500 mg/Lcarbenicillin and 0.02 mM glyphosate. These tissues were transferred tofresh media every two weeks. Plantlets with elongated meristems androots can be regenerated from embryogenic callus tissue any time duringthe culture period. Once the root system was established, the plantswere transferred to soil and subsequently assayed. All the plantsoriginating from the same infected precultured immature embryo or calluswere considered as siblings from the same transgenic event.

Example 18 Evaluation of Transgenic Arabidopsis for Seed Yield and PlantGrowth Rate Under Normal Conditions in Greenhouse Assays (GH-SM Assays)

Assay 1: Seed Yield Plant Biomass and Plant Growth Rate Under NormalGreenhouse Conditions—

This assay follows seed yield production, the biomass formation and therosette area growth of plants grown in the greenhouse at non-limitingnitrogen growth conditions. Transgenic Arabidopsis seeds were sown inagar media supplemented with ½ MS medium and a selection agent(Kanamycin). The T2 transgenic seedlings were then transplanted to 1.7trays filled with peat and perlite in a 1:1 ratio. The trays wereirrigated with a solution containing 6 mM inorganic nitrogen in the formof KNO₃ with 1 mM KH₂PO₄, 1 mM MgSO₄, 2 mM CaCl₂ and microelements. Allplants were grown in the greenhouse until mature seeds. Seeds wereharvested, extracted and weighted. The remaining plant biomass (theabove ground tissue) was also harvested, and weighted immediately orfollowing drying in oven at 50° C. for 24 hours.

Each construct was validated at its T2 generation. Transgenic plantstransformed with a construct conformed by an empty vector carrying theAt6669 promoter and the selection marker were used as control.

The plants were analyzed for their overall size, growth rate, flowering,seed yield, 1.000-seed weight, dry matter and harvest index (HI—seedyield/dry matter). Transgenic plants performance was compared to controlplants grown in parallel under the same conditions. Mock-transgenicplants expressing the uidA reporter gene (GUS-Intron) or with no gene atall, under the same promoter were used as control.

The experiment was planned in nested randomized plot distribution. Foreach gene of the invention three to five independent transformationevents were analyzed from each construct.

Digital Imaging—

A laboratory image acquisition system, which consists of a digitalreflex camera (Canon EOS 300D) attached with a 55 mm focal length lens(Canon EF-S series), mounted on a reproduction device (Kaiser RS), whichincludes 4 light units (4×150 Watts light bulb) was used for capturingimages of plant samples.

The image capturing process was repeated every 2 days starting from day1 after transplanting till day 15. Same camera, placed in a custom madeiron mount, was used for capturing images of larger plants sawn in whitetubs in an environmental controlled greenhouse. The tubs were squareshape include 1.7 liter trays. During the capture process, the tubs wereplaced beneath the iron mount, while avoiding direct sun light andcasting of shadows.

An image analysis system was used, which consists of a personal desktopcomputer (Intel P4 3.0 GHz processor) and a public domain program—ImageJ1.39 [Java based image processing program which was developed at theU.S. National Institutes of Health and freely available on the internetat Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/]. Imageswere captured in resolution of 10 Mega Pixels (3888×2592 pixels) andstored in a low compression JPEG (Joint Photographic Experts Groupstandard) format. Next, analyzed data was saved to text files andprocessed using the JMP statistical analysis software (SAS institute).

Leaf Analysis—

Using the digital analysis leaves data was and is calculated, includingleaf number, rosette area, rosette diameter, and leaf blade area.

Vegetative Growth Rate:

the (GR) of leaf number [Formula VI (described above)], rosette area(Formula XIX below), plot coverage (Formula XX below) and harvest index(Formula IV above) was calculated with the indicated formulas.Growth rate of rosette area=Regression coefficient of rosette area alongtime course.  Formula XIXGR plot coverage Growth rate of plot coverage=Regression coefficient ofplot coverage along time course.  Formula XXGrowth rate (GR) rosette diameter−Regression coefficient of rosettediameter along time course.  Formula XXIV

Seeds Average Weight—

At the end of the experiment all seeds were collected. The seeds arescattered on a glass tray and a picture was taken. Using the digitalanalysis, the number of seeds in each sample was calculated.

Dry Weight and Seed Yield—

On about day 80 from sowing, the plants were harvested and left to dryat 30° C. in a drying chamber. The biomass and seed weight of each plotwere measured and divided by the number of plants in each plot.

Dry weight=total weight of the vegetative portion above ground(excluding roots) after drying at 30° C. in a drying chamber;

Seed yield per plant=total seed weight per plant (Gr.).

1000 seed weight (the weight of 1000 seeds) (Gr.).

Oil Percentage in Seeds—

At the end of the experiment all seeds from each plot were collected.Seeds from 3 plots were mixed grounded and then mounted onto theextraction chamber. 210 ml of n-Hexane (Cat No. 080951 Biolab Ltd.) wereused as the solvent. The extraction was performed for 30 hours at mediumheat 50° C. Once the extraction has ended the n-Hexane is evaporatedusing the evaporator at 35° C., and vacuum conditions. The process wasrepeated twice. The information gained from the Soxhlet extractor(Soxhlet, F. Die gewichtsanalytische Bestimmung des Milchfettes,Polytechnisches J. (Dingler's) 1879, 232, 461) was used to create acalibration curve for the Low Resonance NMR. The content of oil of allseed samples was determined using the Low Resonance NMR (MARANUltra-Oxford Instrument) and its MultiQuant software package.

Silique Length Analysis—

On day 50 from sowing, 30 siliques from different plants in each plotwere sampled in block A. The chosen siliques were green-yellow in colorand were collected from the bottom parts of a grown plant's stem. Adigital photograph was taken to determine silique's length.

Statistical Analyses—

To identify outperforming genes and constructs, results from theindependent transformation events tested were analyzed separately. Datawas analyzed using Student's t-test and results were consideredsignificant if the p value was less than 0.1. The JMP statisticssoftware package was used (Version 5.2.1, SAS Institute Inc., Cary.N.C., USA).

Experimental Results:

Tables 55-59 summarize the observed phenotypes of transgenic plantsexpressing the genes constructs using the GH-SM Assays.

The genes listed in Tables 55-59 improved plant performance when grownat normal conditions. These genes produced larger plants with a largerphotosynthetic area, leaf number, biomass (dry weight, rosette diameter,rosette area and plot coverage, leaf blade area), growth rate (e.g., ofleaf number, plot coverage and rosette diameter), blade relative area,yield (e.g., harvest index, seed yield, 1000 seed weight), as well asinflorescence emergence. The genes were cloned under the regulation of aconstitutive At6669 promoter (SEQ ID NO:9405). The evaluation of eachgene was performed by testing the performance of different number ofevents. Event with p-value<0.1 was considered statistically significant.

TABLE 55 Genes showing improved plant performance at normal growthconditions under regulation of At6669 promoter Inflorescence Dry Weight[mg] Flowering [days] Emergence [days] Gene Name Event # Ave. P-Val. %Incr. Ave. P-Val. % Incr. Ave. P-Val. % Incr. WYM7 71168.1 — — — 22.60.03 −4 15.5 0.20 −3 WYM17 71315.1 — — — 23.1 0.20 −2 — — — WYM5271463.1 709.9 0.12 9 22.9 0.08 −3 — — — WYM106 71687.6 677.1 0.25 4 — —— — — — WYM110 71443.5 — — — 23.1 0.21 −2 — — — WYM52 71461.2 — — — 22.50.02 −5 15.6 0.23 −3 WYM77 70947.1 707.5 0.09 8 — — — — — — WYM10671685.3 697.5 0.13 7 23.1 0.19 −2 — — — CONT. — 652.2 — — 23.6 — — 16.0— — WYM47 69683.5 724.6 0.23 3 22.2 L −5 — — — WYM80 69995.1 736.0 0.175 23.1 0.24 −1 — — — WYM80 69994.1 — — — 22.8 0.08 −2 — — — WYM7770947.4 728.5 0.18 4 — — — 15.4 0.21 0 WYM80 69995.4 — — — 22.7 0.06 −3— — — CONT. — 703.6 — — 23.4 — — 15.5 — — WYM26 71627.6 774.2 0.03 11 —— — — — — WYM110 71443.1 730.6 0.20 5 — — — — — — WYM77 70949.3 747.00.16 7 — — — — — — WYM77 70947.2 — — — 21.4 L −7 15.3 0.19 −1 WYM9570178.4 — — — 22.6 0.24 −1 — — — WYM17 71314.3 741.6 0.10 7 22.5 0.15 −2— — — CONT. — 695.5 — — 22.9 — — 15.4 — — WYM17 71315.2 780.9 0.16 821.9 0.17 −3 — — — WYM95 70180.2 786.8 0.11 9 — — — — — — WYM7 71169.7 —— — 22.0 0.21 −2 — — — WYM7 71170.1 — — — 22.1 0.23 −2 — — — WYM9570181.2 — — — 21.9 0.20 −3 15.3 0.29 −1 CONT. — 721.4 — — 22.5 — — 15.4— — WYM80 69993.2 723.3 0.03 16 — — — 15.5 0.20 −2 WYM95 70182.3 655.40.17 5 21.5 0.02 −5 15.5 0.20 −2 WYM17 71313.9 687.1 0.08 10 — — — 15.40.15 −2 WYM95 70182.5 710.0 0.02 14 21.9 0.07 −3 15.5 0.20 −2 WYM4769685.5 675.4 0.09 8 21.9 0.07 −3 15.5 0.20 −2 WYM17 71316.2 — — — 21.40.03 −5 15.3 0.12 −3 WYM95 70178.1 685.8 0.05 10 21.9 0.10 −3 15.5 0.20−2 CONT. — 625.0 — — 22.6 — — 15.8 — — WYM106 71684.4 690.0 0.13 7 — — —— — — WYM110 71442.5 739.5 0.03 14 21.1 L −7 15.3 0.05 −1 WYM47 69681.4— — — 21.7 0.06 −4 15.3 0.16 −1 WYM47 69685.3 677.4 0.20 5 21.6 0.02 −515.5 0.20 0 WYM26 71627.4 694.8 0.09 7 — — — — — — WYM26 71626.6 699.20.08 8 — — — — — — WYM110 71445.5 684.1 0.20 6 — — — — — — WYM10671687.1 697.5 0.08 8 — — — 15.5 0.20 0 CONT. — 647.8 — — 22.7 — — 15.6 —— WYM52 71463.4 — — — 22.6 0.02 −5 15.6 0.11 −5 WYM110 71445.6 — — —22.8 0.06 −4 15.8 0.17 −4 WYM44 71321.3 704.2 0.28 3 22.8 0.04 −4 — — —WYM77 70948.2 — — — 23.0 0.10 −3 — — — WYM26 71623.2 749.0 0.07 9 23.30.26 −2 — — — WYM80 69994.2 738.4 0.21 8 22.5 0.02 −5 15.5 0.10 −6WYM110 71443.6 720.3 0.23 5 23.1 0.11 −3 15.7 0.13 −5 WYM17 71313.6 — —— 23.1 0.12 −2 15.5 0.10 −6 CONT. — 685.7 — — 23.7 — — 16.4 — — WYM9570181.1 — — — 23.1 0.03 −4 — — — WYM47 69685.1 712.9 0.03 7 22.6 L −6 —— — WYM95 70183.2 747.7 0.03 12 23.0 0.03 −4 — — — WYM47 69683.3 683.90.12 7 22.4 L −7 — — — WYM95 70181.3 — — — 22.6 L −6 — — — WYM80 69994.4738.4 L 10 23.0 0.02 −5 — — — WYM26 71622.3 777.9 0.03 16 23.5 0.23 −2 —— — WYM77 70949.1 703.4 0.19 5 23.6 0.12 −2 — — — CONT. — 669.3 — — 24.1— — 15.4 — — WYM52 71465.5 820.0 0.24 3 22.0 0.04 −3 15.4 0.21 0 WYM4471317.1 — — — 22.5 0.15 −1 — — — CONT. — 794.2 — — 22.8 — — 15.5 — —WYM7 71169.2 932.5 0.04 22 21.3 L −6 15.4 0.19 −1 WYM52 71461.6 806.40.21 5 22.3 0.22 −1 — — — WYM17 71313.4 — — — 22.3 0.23 −1 — — — WYM9570181.6 840.0 0.15 10 — — — — — — CONT. — 766.1 — — 22.6 — — 15.4 — —WYM17 71315.4 — — — 22.1 0.22 −2 — — — CONT. — 809.5 — — 22.4 — — 15.4 —— WYM44 71322.4 — — — — — — 15.4 0.12 −1 WYM110 71444.4 — — — 21.3 0.06−2 — — — WYM7 71170.5 — — — — — — 15.4 0.23 −1 WYM7 71170.3 — — — 21.50.18 −1 — — — WYM106 71685.6 — — — — — — 15.4 0.12 −1 WYM52 71463.6812.5 0.14 7 21.0 0.13 −4 14.7 0.14 −5 WYM17 71314.4 812.0 0.11 7 21.60.27 −1 15.5 0.20 0 CONT. — 762.2 — — 21.8 — — 15.6 — — WYM52 71461.5 —— — 21.5 0.18 −3 15.2 0.06 −4 WYM106 71687.3 — — — 21.8 0.22 −2 15.60.26 −1 WYM52 71465.2 — — — 21.5 0.13 −3 15.4 0.15 −2 WYM7 71170.2 — — —21.9 0.28 −2 15.4 0.12 −3 WYMI10 71445.1 792.1 0.05 7 21.3 0.10 −4 15.30.09 −3 WYM52 71465.4 767.3 0.19 3 21.7 0.19 −3 15.5 0.20 −2 WYM4471321.5 774.6 0.19 4 20.7 0.03 −7 15.4 0.15 −2 WYM44 71317.8 — — — 21.70.21 −2 15.5 0.20 −2 CONT. — 741.5 — — 22.2 — — 15.8 — — WYM44 71322.6 —— — 22.4 0.10 −3 — — — WYM26 71626.4 871.9 0.08 11 22.8 0.25 −2 — — —WYM47 69684.3 — — — 21.9 0.03 −5 — — — WYM110 71445.2 — — — 22.6 0.14 −2— — — CONT. — 782.8 — — 23.1 — — 15.4 — — WYM92 70001.1 — — — 19.6 0.11−4 — — — WYM60 69869.3 577.4 0.19 8 20.2 0.28 −2 15.3 0.07 −4 WYM6369984.3 — — — 19.8 0.16 −3 15.4 0.17 −4 CONT. — 535.4 — — 20.5 — — 16.0— — WYM37 70944.7 — — — 19.8 0.16 −2 — — — WYM57 69512.7 — — — 19.9 0.05−2 — — — WYM37 70942.4 — — — 20.1 0.19 −1 — — — WYM27 69935.2 — — — 19.70.12 −3 — — — WYM58 69959.3 — — — 20.0 0.13 −2 — — — WYM63 69984.2 — — —19.2 0.07 −5 — — — WYM60 69870.2 — — — 19.9 0.24 −2 — — — CONT. — 544.7— — 20.3 — — 15.1 — — WYM63 69982.4 — — — 17.8 L −10 14.1 0.14 −1 WYM2769936.2 — — — 18.5 0.01 −6 14.1 0.20 −1 WYM51 69954.2 — — — 18.9 0.02 −414.0 0.09 −2 WYM92 70003.1 553.8 0.22 5 19.0 0.18 −3 — — — LYM90 69389.5— — — 18.1 L −8 14.1 0.20 −1 WYM60 69870.8 — — — 19.2 0.10 −2 — — —WYM51 69950.5 — — — 18.0 L −9 14.0 0.09 −2 WYM27 69937.5 — — — 19.4 0.23−2 — — — CONT. — 529.7 — — 19.7 — — 14.3 — — WYM60 69869.2 — — — 19.90.14 −3 — — — WYM58 69960.2 674.2 0.30 4 19.9 0.13 −3 — — — WYM5169950.1 — — — 19.6 0.07 −5 14.9 0.12 −8 WYM92 70000.5 — — — 19.6 0.14 −415.2 0.11 −7 WYM58 69961.10 — — — 20.1 0.19 −2 15.5 0.13 −5 WYM6369983.2 — — — 20.0 0.17 −3 — — — WYM63 69980.3 — — — — — — 15.5 0.22 −5CONT. — 650.7 — — 20.6 — — 16.3 — — WYM92 69998.2 — — — — — — 15.9 0.20−3 LYM90 69389.1 618.8 0.26 3 — — — — — — WYM63 69982.1 625.2 0.12 419.3 0.02 −7 14.9 0.02 −9 WYM37 70942.3 615.4 0.25 2 — — — — — — WYM6369984.6 — — — 20.0 L −4 15.7 0.01 −4 WYM51 69953.4 — — — 20.4 0.17 −2 —— — WYM60 69868.3 — — — 20.1 L −4 15.8 0.08 −3 WYM66 70175.3 — — — 20.1L −4 16.2 0.26 −1 CONT. — 600.7 — — 20.9 — — 16.3 — — WYM37 70942.6670.1 0.06 13 20.2 0.08 −2 — — — WYM57 69514.2 666.7 0.05 12 18.1 L −1214.0 L −13 WYM66 70176.2 656.3 0.05 10 19.7 0.07 −4 14.5 0.04 −10 WYM9270000.3 633.4 0.12 7 18.8 L −9 14.6 0.04 −10 WYM60 69867.2 730.0 L 23 —— — — — — WYM60 69870.3 — — — 19.3 0.06 −6 14.7 0.04 −9 WYM33 69938.11 —— — 20.0 0.11 −3 — — — CONT. — 594.1 — — 20.6 — — 16.2 — — WYM57 69517.1680.8 0.04 15 20.2 0.12 −2 14.5 0.04 −11 WYM60 69868.5 643.0 0.02 9 — —— 16.1 0.15 −1 WYM58 69961.9 641.8 0.13 9 20.3 0.12 −1 15.2 0.13 −6WYM27 69935.9 615.4 0.17 4 20.2 0.08 −2 15.8 0.10 −3 WYM66 70174.4 — — —— — — 15.3 0.14 −6 WYM33 69942.2 640.4 0.12 8 — — — 15.6 L −4 WYM3369942.1 678.4 0.02 15 20.2 0.08 −2 14.4 L −12 WYM57 69515.4 618.0 0.23 518.5 L −10 14.0 L −14 CONT. — 591.1 — — 20.6 — — 16.3 — — WYM57 69514.3667.9 0.19 6 19.7 0.06 −4 15.6 0.20 −4 WYM57 69513.3 696.7 0.06 10 19.30.04 −6 14.4 L −11 LYM90 69388.2 677.9 0.21 7 — — — 15.4 0.09 −5 WYM6069867.3 675.9 0.12 7 20.1 0.12 −2 15.3 0.11 −6 WYM37 70939.4 — — — 20.30.24 −1 — — — CONT. — 632.2 — — 20.5 — — 16.2 — — WYM37 70942.5 669.2 L9 — — — — — — WYM33 69938.6 685.2 0.02 12 — — — — — — WYM58 69959.5635.0 0.23 3 — — — — — — WYM58 69960.7 627.9 0.21 2 19.3 L −6 14.9 0.12−6 WYM57 69515.1 — — — 20.4 0.20 −1 — — — WYM27 69935.4 654.1 0.12 720.3 0.09 −1 — — — CONT. — 614.1 — — 20.5 — — 15.9 — — WYM66 70174.3 — —— 19.6 0.02 −4 — — — WYM33 69943.2 — — — — — — 15.2 0.05 −4 LYM9069388.5 661.3 0.13 10 20.3 0.29 −1 15.0 L −5 WYM58 69960.3 — — — 19.70.08 −3 — — — CONT. — 601.2 — — 20.4 — — 15.8 — — WYM33 69938.7 — — —20.2 0.04 −2 — — — WYM92 69999.2 — — — 20.3 0.13 −2 — — — LYM90 69389.3578.3 0.27 3 — — — — — — CONT. — 563.8 — — 20.7 — — 15.5 — — LYM9069386.2 — — — 19.7 L −3 15.0 0.21 −3 LYM90 69386.3 — — — 20.0 0.23 −214.7 0.15 −5 WYM27 69936.1 — — — 19.1 0.06 −6 14.7 0.19 −5 LYM90 69388.4— — — 19.8 0.04 −3 14.6 0.13 −6 WYM33 69939.1 — — — 20.2 0.25 −1 14.90.24 −4 WYM66 70175.4 613.4 0.16 4 19.2 0.06 −6 14.0 0.03 −9 CONT. —589.0 — — 20.4 — — 15.5 — — WYM60 69870.5 631.3 0.03 4 19.3 0.01 −6 14.10.14 −3 WYM51 69954.4 — — — 19.3 0.02 −6 14.1 0.14 −3 WYM66 70176.1 — —— 20.2 0.12 −2 — — — WYM58 69961.3 — — — 20.0 0.08 −3 14.0 0.10 -4 WYM5869960.1 — — — 20.3 0.27 −1 — — — CONT. — 609.6 — — 20.5 — — 14.6 — —WYM58 69961.7 — — — 19.1 0.13 −3 — — — WYM92 70000.4 — — — 18.4 L −7 — —— WYM51 69954.7 — — — 17.8 L −10 14.0 0.08 −7 WYM57 69513.2 — — — 18.20.02 −8 14.0 0.08 −7 WYM66 70175.2 — — — 18.8 0.02 −5 14.0 0.08 −7 WYM6670173.1 — — — 18.4 0.01 −7 — — — CONT. — 609.2 — — 19.7 — — 15.0 — —WYM108 69633.1 764.7 0.02 18 — — — — — — WYM4 69736.6 679.4 0.13 5 — — —— — — WYM13 69646.1 716.7 0.01 11 18.4 0.02 −11 — — — WYM98 70008.2666.3 0.14 3 20.1 0.13 −3 — — — LNU74_H109 69484.1 698.2 0.03 8 19.3 L−7 — — — WYM13 69647.3 691.3 0.02 7 — — — — — — WYM99 70020.4 686.3 0.126 20.3 0.29 −2 — — — CONT. — 648.5 — — 20.8 — — 15.0 — — WYM108 69635.1— — — — — — 15.0 0.20 0 WYM84 69860.1 678.0 0.17 7 20.0 0.18 −2 15.00.20 0 WYM11 69639.7 683.8 0.18 8 — — — — — — WYM101 69715.3 680.0 0.188 — — — 15.0 0.20 0 WYM11 69642.2 681.3 0.16 8 — — — 15.0 0.20 0 WYM8469865.2 — — — 19.7 0.08 −4 15.0 0.20 0 LNU74_H109 69485.3 760.0 0.02 20— — — 15.0 0.20 0 WYM11 69639.9 670.0 0.22 6 19.8 0.11 −3 15.0 0.20 0CONT. — 632.5 — — 20.4 — — 15.0 — — WYM99 70020.3 — — — 20.6 0.07 −5 — —— WYM99 70016.3 — — — 20.5 0.12 −5 — — — WYM109 69717.3 — — — 20.1 0.07−7 — — — WYM108 69634.1 — — — 20.4 0.06 −5 — — — WYM84 69864.5 — — —21.0 0.17 −3 — — — CONT. — 700.0 — — 21.6 — — 15.0 — — WYM98 70009.1 — —— 20.2 0.14 −2 — — — WYM4 69737.3 — — — 20.3 0.26 −1 — — — WYM9970016.10 771.6 0.15 7 — — — — — — CONT. — 722.2 — — 20.6 — — 15.0 — —WYM109 69720.7 781.7 0.06 11 20.8 0.16 −3 — — — LNU74_H109 69485.1 — — —20.2 0.02 −6 — — — WYM11 69640.1 — — — 20.7 0.10 −3 — — — CONT. — 701.5— — 21.4 — — 15.0 — — WYM4 69734.2 — — — 19.9 0.05 −4 — — — WYM4 69736.3— — — 20.0 0.05 −4 — — — WYM100 69872.5 771.7 0.22 5 20.0 0.06 −3 — — —WYM13 69646.2 — — — 20.2 0.20 −3 — — — WYM13 69645.2 760.9 0.28 4 19.70.02 −5 — — — WYM99 70016.8 — — — 19.4 L −6 — — — WYM109 69716.3 — — —20.3 0.20 −2 — — — WYM109 69720.6 — — — 19.8 0.03 −5 — — — CONT. — 734.7— — 20.7 — — 15.0 — — WYM109 69716.1 — — — 19.9 0.02 −5 — — — WYM469735.3 — — — 19.8 0.01 −6 — — — WYM101 69710.2 704.2 0.12 12 20.2 0.07−4 — — — LNU74_H109 69483.3 704.6 L 12 19.5 0.07 −7 — — — WYM108 69636.5— — — 20.1 0.03 −4 — — — WYM101 69712.2 — — — 20.5 0.21 −2 — — — WYM469736.1 — — — 20.0 0.03 −5 — — — WYM98 70008.3 — — — 19.5 L −7 — — —CONT. — 626.6 — — 21.0 — — 15.0 — — WYM11 69641.1 — — — 20.3 0.08 −3 — —— WYM98 70009.3 — — — 19.6 0.02 −6 — — — WYM13 69647.7 728.3 0.27 4 — —— — — — CONT. — 700.1 — — 21.0 — — 15.0 — — WYM13 69647.9 693.4 0.22 420.3 0.18 −3 — — — WYM13 69644.2 — — — 20.4 0.19 −3 — — — WYM98 70008.1— — — 20.0 0.04 −5 — — — WYM101 69715.5 732.5 0.06 10 19.8 0.02 −6 — — —WYM98 70005.3 — — — 19.9 0.03 −5 — — — CONT. — 663.8 — — 21.0 — — 15.0 —— WYM11 69641.2 — — — 21.0 0.11 −3 — — — WYM98 70005.2 — — — 20.3 0.02−6 — — — LNU74_H109 69483.4 732.5 0.26 4 19.9 L −8 — — — CONT. — 707.6 —— 21.6 — — 15.0 — — LNU74_H109 69482.1 703.8 0.16 3 — — — — — —LNU74_H109 69482.2 — — — 21.2 0.15 −2 — — — WYM98 70008.4 — — — 21.00.16 −3 — — — CONT. — 682.5 — — 21.7 — — 15.0 — — WYM100 69876.2 712.10.13 4 — — — — — — WYMI3 69645.5 — — — 20.9 0.22 −2 — — — WYM13 69647.1732.5 0.03 7 21.0 0.22 −1 — — — CONT. — 681.7 — — 21.3 — — 15.0 — —WYM99 70016.9 726.4 0.27 5 21.3 0.07 −2 — — — WYM13 69647.4 — — — 20.00.05 −8 — — — WYM109 69719.2 — — — 21.0 0.14 −3 — — — WYM101 69715.2 — —— 21.4 0.19 −1 — — — WYM11 69638.1 — — — 21.0 0.02 −3 — — — WYM9970016.2 — — — 21.3 0.17 −1 — — — WYM84 69864.1 — — — 21.3 0.15 −2 — — —CONT. — 692.9 — — 21.7 — — 15.0 — — WYM99 70017.4 — — — 19.6 0.03 −6 — —— WYM 108 69633.3 — — — 20.6 0.28 −1 — — — CONT. — 717.5 — — 20.9 — —15.0 — — Table 55. “CONT.” - Control; “Ave.” - Average; “% Incr.” = %increment; “p-val.” - p-value, L - p < 0.01.

TABLE 56 Genes showing improved plant performance at normal growthconditions under regulation of At6669 promoter Leaf Blade Area [cm²]Leaf Number Gene Name Event # Ave. P-Val. % Incr. Ave. P-Val. % Incr.WYM7 71168.1 1.2 0.06 13 11.3 0.03 7 WYM17 71315.1 1.2 0.02 10 10.7 0.242 WYM106 71687.6 1.1 0.15 6 11.2 0.02 6 WYM52 71461.2 1.1 0.06 8 — — —WYM77 70947.1 1.1 0.24 5 — — — WYM106 71685.3 1.2 0.02 17 11.0 0.04 5CONT. — 1.1 — — 10.5 — — WYM47 69683.5 1.1 0.04 11 — — — CONT. — 1.0 — —10.3 — — WYM26 71627.6 1.0 0.29 4 — — — CONT. — 1.0 — — 10.3 — — WYM1771315.2 — — — 11.6 L 4 WYM7 71169.7 — — — 11.5 0.11 3 WYM77 70946.7 — —— 11.4 0.16 2 WYM7 71170.1 — — — 11.4 0.28 3 WYM95 70181.2 1.5 0.29 6 —— — CONT. — 1.4 — — 11.1 — — WYM95 70178.1 — — — 10.2 0.26 1 CONT. — 1.0— — 10.1 — — WYM106 71684.4 1.0 0.21 6 — — — WYM110 71442.5 1.1 0.03 2411.1 0.03 15 WYM47 69681.4 1.0 0.12 13 10.0 0.12 4 WYM26 71627.4 1.00.27 7 — — — WYM26 71626.6 1.0 0.27 6 9.8 0.25 2 WYM110 71445.5 1.0 0.158 — — — WYM106 71687.1 1.0 0.14 8 — — — CONT. — 0.9 — — 9.6 — — WYM5271463.4 1.2 0.05 21 10.8 0.17 6 WYM110 71445.6 1.2 0.09 14 11.3 L 10WYM44 71321.3 1.3 0.03 25 10.8 L 6 WYM77 70948.2 1.2 0.07 20 11.2 0.0610 WYM26 71623.2 1.3 0.02 25 11.0 L 8 WYM80 69994.2 1.3 0.01 32 11.3 L11 WYM110 71443.6 1.2 0.08 16 10.7 0.18 5 WYM17 71313.6 1.2 0.09 15 10.8L 6 CONT. — 1.0 — — 10.2 — — WYM47 69685.1 1.1 0.23 7 10.3 0.28 3 WYM9570183.2 — — — 10.2 0.24 2 WYM47 69683.3 1.1 0.28 4 10.3 0.25 4 WYM9570181.3 — — — 10.2 0.21 3 WYM80 69994.4 1.1 0.16 9 10.8 L 9 WYM2671622.3 — — — 10.5 0.13 6 CONT. — 1.0 — — 9.9 — — WYM26 71626.1 1.3 0.274 11.2 0.14 4 WYM52 71465.5 1.3 0.11 8 11.3 0.12 5 CONT. — 1.2 — — 10.8— — WYM7 71169.2 1.3 0.10 13 11.4 0.22 3 CONT. — 1.2 — — 11.1 — — WYM2671626.2 — — — 10.8 0.19 3 WYM77 70948.5 — — — 11.0 0.13 5 WYM17 71315.41.2 0.23 7 10.7 0.24 2 CONT. — 1.1 — — 10.5 — — WYM7 71170.3 1.2 0.16 1110.8 0.20 2 WYM106 71685.6 1.2 0.30 6 — — — WYM52 71463.6 1.3 0.19 13 —— — CONT. — 1.1 — — 10.6 — — WYM52 71461.5 1.1 0.18 10 10.4 0.26 4WYM106 71687.3 1.2 0.02 17 11.2 0.01 11 WYM52 71465.2 1.1 0.18 6 11.20.03 11 WYM7 71170.2 1.1 0.29 8 — — — WYMI10 71445.1 1.2 0.02 20 10.70.05 6 WYM52 71465.4 1.2 0.07 11 10.7 0.06 6 WYM44 71321.5 1.4 L 32 11.00.02 9 WYM44 71317.8 1.1 0.12 11 10.5 0.17 4 CONT. — 1.0 — — 10.1 — —WYM44 71322.6 1.3 0.28 6 — — — WYM26 71626.4 1.3 0.08 11 11.3 0.11 7WYM47 69684.3 1.3 0.09 12 11.4 0.03 8 CONT. — 1.2 — — 10.6 — — WYM9270001.1 1.3 0.15 11 — — — WYM63 69983.1 — — — 10.3 0.08 2 WYM60 69869.31.2 0.26 7 10.2 0.18 1 WYM63 69982.7 — — — 10.3 0.08 2 CONT. — 1.1 — —10.1 — — WYM37 70944.7 1.3 0.11 12 10.6 0.01 7 WYM57 69512.7 1.2 0.14 910.5 0.06 5 WYM37 70942.4 1.3 0.04 16 10.9 0.02 10 WYM27 69935.2 1.30.12 10 10.3 0.13 4 WYM58 69959.3 1.2 0.26 5 10.5 0.22 6 WYM63 69984.21.2 0.16 8 10.6 0.20 6 WYM60 69870.2 — — — 10.3 0.05 4 CONT. — 1.1 — —9.9 — — WYM63 69982.4 1.5 L 35 10.6 0.17 5 WYM27 69936.2 1.3 L 12 11.3 L11 WYM51 69954.2 1.3 0.07 14 10.9 0.01 7 WYM92 70003.1 1.4 L 18 10.60.14 5 LYM90 69389.5 1.3 L 16 11.0 L 9 WYM60 69870.8 1.4 L 25 — — —WYM51 69950.5 1.3 0.08 9 10.7 0.21 5 WYM27 69937.5 1.3 0.04 9 10.8 0.026 CONT. — 1.2 — — 10.1 — — WYM51 69950.1 1.3 0.09 13 11.4 0.08 7 CONT. —1.2 — — 10.7 — — WYM92 69998.2 1.1 0.20 6 10.4 0.03 5 WYM63 69982.1 1.3L 18 10.9 0.04 10 WYM37 70942.3 1.1 0.24 6 — — — WYM63 69984.6 — — —10.2 0.20 3 WYM60 69868.3 1.2 0.06 8 10.7 L 8 WYM66 70175.3 1.2 0.23 810.3 0.06 4 CONT. — 1.1 — — 9.9 — — WYM37 70942.6 1.6 0.04 26 11.3 0.027 WYM57 69514.2 1.8 L 44 10.9 0.26 2 WYM66 70176.2 1.6 0.02 24 11.2 0.055 WYM92 70000.3 1.7 0.01 35 11.1 0.05 4 WYM60 69867.2 1.8 L 38 11.6 0.029 WYM60 69870.3 1.5 0.09 19 11.5 0.07 8 WYM33 69938.11 — — — 10.9 0.27 2WYM66 70174.1 1.5 0.07 16 11.1 0.22 4 CONT. — 1.3 — — 10.6 — — WYM5769517.1 1.6 L 28 10.9 0.27 3 WYM60 69868.5 1.6 L 26 11.1 0.16 5 WYM5869961.9 1.5 0.05 18 11.4 0.15 7 WYM27 69935.9 1.5 0.04 19 11.1 0.11 5WYM66 70174.4 1.6 0.03 27 11.2 0.05 6 WYM33 69942.2 1.5 L 17 — — — WYM3369942.1 1.6 0.05 21 11.8 L 12 WYM57 69515.4 1.8 L 41 10.9 0.29 3 CONT. —1.3 — — 10.6 — — WYM57 69514.3 1.3 0.12 17 — — — WYM57 69513.3 1.3 0.0320 — — — LYM90 69388.2 1.4 0.03 26 — — — WYM51 69954.1 1.2 0.27 5 — — —WYM60 69867.3 1.3 0.05 18 — — — WYM27 69937.1 1.2 0.25 8 — — — LYM9069389.6 1.2 0.27 5 — — — CONT. — 1.1 — — 10.8 — — WYM37 70942.5 1.5 0.0318 11.2 L 8 WYM58 69960.7 1.5 0.06 17 11.0 L 6 WYM57 69515.1 1.3 0.24 610.6 0.04 3 WYM27 69935.4 — — — 10.6 0.15 2 CONT. — 1.3 — — 10.3 — —WYM92 70000.9 — — — 10.8 0.06 4 WYM66 70174.3 1.4 0.26 6 — — — WYM3369943.2 — — — 10.8 0.13 4 LYM90 69388.5 1.6 0.04 18 11.0 0.17 6 WYM5169950.3 1.4 0.28 5 11.0 0.06 6 CONT. — 1.3 — — 10.4 — — WYM66 70177.7 —— — 10.8 0.10 5 CONT. — 1.2 — — 10.3 — — LYM90 69386.3 1.5 0.06 18 — — —LYM90 69388.4 1.4 0.13 11 11.3 0.28 1 WYM66 70175.4 1.4 0.26 9 — — —CONT. — 1.3 — — 11.1 — — WYM92 70003.2 — — — 11.2 0.08 5 WYM60 69870.51.5 0.10 11 — — — LYM90 69390.2 — — — 10.9 0.25 3 WYM58 69961.3 1.4 0.226 11.0 0.22 4 CONT. — 1.4 — — 10.6 — — WYM51 69953.5 — — — 10.4 0.21 2WYM58 69961.7 1.2 0.22 9 10.8 0.11 5 WYM92 70000.4 1.2 0.19 8 — — —WYM51 69954.7 1.2 0.25 5 11.3 L 11 WYM57 69513.2 1.2 0.13 8 — — — WYM3770944.2 1.2 0.22 7 — — — WYM66 70175.2 1.2 0.20 6 11.1 0.03 8 WYM6670173.1 1.3 0.07 15 11.2 0.09 9 CONT. — 1.1 — — 10.3 — — WYM108 69633.11.0 0.05 5 9.6 0.29 3 WYM4 69736.6 — — — 9.6 0.19 3 WYM13 69646.1 1.2 L25 10.1 0.05 9 WYM98 70008.2 1.1 0.01 11 9.8 0.06 5 LNU74_H109 69484.11.0 0.04 7 9.7 0.09 4 WYM99 70020.4 1.0 0.17 7 9.6 0.23 3 CONT. — 1.0 —— 9.3 — — WYM108 69635.1 1.1 0.08 10 — — — WYM84 69860.1 1.2 0.02 1510.0 0.18 5 WYM101 69715.3 1.0 0.21 4 — — — WYM11 69642.2 1.1 0.08 11 —— — WYM84 69865.2 1.2 0.04 17 9.8 0.25 3 LNU74_H109 69485.3 1.1 0.07 8 —— — WYM 11 69639.9 1.3 L 31 10.3 0.07 8 CONT. — 1.0 — — 9.5 — — WYM9970020.3 1.0 0.02 14 9.5 0.20 2 WYM99 70016.3 1.0 L 13 9.8 0.03 5 WYM1169640.3 1.0 0.29 4 9.5 0.27 2 WYM101 69712.3 1.0 0.05 7 9.5 0.18 2WYM109 69717.3 1.1 0.05 19 9.8 0.03 5 WYM84 69862.1 — — — 9.7 0.05 4WYM108 69634.1 1.0 L 11 9.7 0.08 4 WYM84 69864.5 1.0 L 10 — — — CONT. —0.9 — — 9.3 — — WYM11 69641.3 1.4 0.23 6 — — — WYM98 70009.1 — — — 10.8L 15 WYM4 69737.3 — — — 9.8 0.17 5 LNU74_H109 69487.1 — — — 10.5 0.09 12WYM100 69873.2 1.4 0.29 6 10.3 0.03 10 WYM101 69713.5 — — — 9.6 0.29 3WYM109 69720.8 — — — 10.2 0.04 9 WYM99 70016.10 — — — 10.3 0.02 10 CONT.— 1.3 — — 9.3 — — WYM109 69720.7 — — — 10.0 0.04 5 WYM101 69715.8 1.30.05 16 — — — WYM108 69632.1 1.3 0.07 24 9.9 0.09 4 WYM108 69636.6 1.2 L15 — — — WYM4 69737.8 1.2 0.09 14 — — — WYM11 69640.1 1.3 L 23 — — —CONT. — 1.1 — — 9.5 — — WYM4 69736.3 1.3 0.20 8 — — — WYM100 69872.5 1.40.01 19 10.8 0.06 5 WYM13 69645.2 1.5 L 25 10.4 0.26 1 WYM99 70016.8 1.30.07 11 10.9 0.02 6 CONT. — 1.2 — — 10.3 — — WYM109 69716.1 — — — 10.60.08 7 WYM101 69710.2 1.3 0.03 10 — — — LNU74_H109 69483.3 1.4 L 15 10.60.07 7 WYM108 69636.5 1.3 0.22 10 10.2 0.27 3 WYM101 69712.2 1.3 0.09 610.3 0.20 4 WYM98 70008.3 1.3 0.16 11 — — — CONT. — 1.2 — — 9.9 — —WYM109 69716.4 1.2 0.26 6 — — — WYM11 69640.7 1.2 0.19 5 — — — WYM1169641.1 1.2 0.03 12 — — — WYM99 70017.5 1.3 L 21 — — — WYM98 70009.3 1.30.02 14 — — — CONT. — 1.1 — — 9.8 — — WYM98 70008.1 1.2 0.16 6 9.9 0.275 WYM101 69715.5 1.2 0.10 7 10.3 0.15 9 WYM84 69864.2 — — — 9.7 0.19 3WYM98 70005.3 — — — 10.1 0.04 8 CONT. — 1.1 — — 9.4 — — WYM100 69874.1 —— — 9.3 0.10 3 WYM11 69641.2 — — — 9.3 0.10 3 WYM98 70005.2 — — — 9.50.11 4 WYM98 70009.6 — — — 9.2 0.26 2 LNU74_H109 69483.4 1.2 0.09 15 9.40.10 4 CONT. — 1.1 — — 9.1 — — WYM4 69739.2 1.0 0.08 10 9.3 0.25 3LNU74_H109 69482.1 1.0 0.03 17 9.4 0.17 4 LNU74_H109 69482.2 0.9 0.22 5— — — WYM108 69635.3 0.9 0.26 5 — — — WYM100 69874.5 1.0 0.12 10 — — —WYM98 70008.4 — — — 9.4 0.18 3 WYM99 70020.1 1.0 0.04 13 — — — CONT. —0.9 — — 9.1 — — WYM101 69714.1 — — — 9.4 0.27 3 WYM 13 69647.1 1.1 0.142 — — — CONT. — 1.0 — — 9.1 — — WYM99 70016.9 1.1 0.25 7 — — — WYM1369647.4 1.2 0.03 12 — — — WYM109 69719.2 1.2 L 16 9.8 0.28 4 WYM10169715.2 1.1 0.12 8 — — — WYM11 69638.1 1.2 0.10 13 — — — WYM84 69864.11.2 0.08 15 10.0 0.22 5 CONT. — 1.0 - - — — — LNU74_H109 69483.5 1.10.20 7 — — — WYM99 70017.4 1.2 0.07 20 — — — WYM108 69635.2 — — — 9.70.10 2 WYM109 69718.2 1.1 0.20 8 — — — CONT. — 1.0 — — 9.5 — — Table 56.“CONT.” - Control; “Ave.” - Average; “% Incr.” = % increment; “p-val.” -p-value, L - p < 0.01.

TABLE 57 Genes showing improved plant performance at normal growthconditions under regulation of At6669 promoter GR Of Rosette Diameter[cm/day] P- % Gene Name Event # Ave. Val. Incr. WYM7 71168.1 0.5 0.06 13WYM17 71315.1 0.5 0.19 7 WYM106 71687.6 0.5 0.05 10 WYM110 71443.5 0.50.21 6 WYM52 71461.2 0.5 0.12 8 WYM106 71685.3 0.5 L 18 CONT. — 0.5 — —WYM47 69683.5 0.5 0.23 8 WYM7 71172.5 0.5 0.26 8 CONT. — 0.4 — — WYM2671627.6 0.5 0.27 12 CONT. — 0.4 — — WYM110 71442.5 0.5 0.05 19 WYM4769681.4 0.4 0.27 11 WYM110 71445.5 0.5 0.19 12 WYM106 71687.1 0.4 0.1711 CONT. — 0.4 — — WYM44 71321.3 0.6 0.07 15 WYM77 70948.2 0.5 0.23 11WYM26 71623.2 0.5 0.13 12 WYM80 69994.2 0.6 0.04 17 CONT. — 0.5 — —WYM47 69683.3 0.5 0.26 12 CONT. — 0.4 — — WYM7 71169.2 0.6 0.19 12 CONT.— 0.5 — — WYM52 71461.5 0.5 0.16 13 WYM106 71687.3 0.5 0.08 15 WYM5271465.2 0.5 0.17 12 WYM110 71445.1 0.5 0.20 11 WYM44 71321.5 0.6 L 26WYM44 71317.8 0.5 0.17 12 CONT. — 0.4 — — WYM44 71322.6 0.5 0.29 9 WYM2671626.4 0.5 0.29 8 CONT. — 0.5 — — WYM92 70001.1 0.5 0.19 12 CONT. — 0.4— — WYM37 70944.7 0.4 0.13 9 WYM57 69512.7 0.4 0.25 8 WYM37 70942.4 0.50.08 12 CONT. — 0.4 — — WYM63 69982.4 0.5 L 22 WYM27 69936.2 0.5 0.08 10WYM92 70003.1 0.5 0.06 9 LYM90 69389.5 0.5 0.04 9 WYM60 69870.8 0.5 0.0411 CONT. — 0.4 — — WYM51 69950.1 0.5 0.28 7 CONT. — 0.4 — — WYM6369982.1 0.4 0.05 12 CONT. — 0.4 — — WYM37 70942.6 0.6 0.06 18 WYM5769514.2 0.6 L 20 WYM66 70176.2 0.6 0.04 17 WYM92 70000.3 0.6 L 25 WYM6069867.2 0.6 L 24 WYM60 69870.3 0.5 0.06 16 WYM66 70174.1 0.5 0.19 10CONT. — 0.5 — — WYM57 69517.1 0.5 0.02 13 WYM60 69868.5 0.6 L 21 WYM5869961.9 0.5 0.09 12 WYM27 69935.9 0.5 0.06 13 WYM66 70174.4 0.5 0.01 17WYM33 69942.2 0.5 0.03 13 WYM33 69942.1 0.5 0.04 13 WYM57 69515.4 0.6 L21 CONT. — 0.5 — — WYM57 69513.3 0.5 0.14 12 LYM90 69388.2 0.5 0.12 13WYM60 69867.3 0.5 0.17 11 CONT. — 0.4 — — WYM37 70942.5 0.5 0.15 9 WYM5869960.7 0.5 0.20 8 CONT. — 0.5 — — LYM90 69388.5 0.5 0.21 9 CONT. — 0.5— — LYM90 69388.4 0.5 0.28 7 CONT. — 0.5 — — WYM66 70175.2 0.5 0.10 10WYM66 70173.1 0.5 0.18 9 CONT. — 0.4 — — WYM13 69646.1 0.5 L 15 WYM9870008.2 0.4 0.02 10 LNU74_H109 69484.1 0.4 0.20 5 WYM99 70020.4 0.4 0.1110 CONT. — 0.4 — — WYM108 69635.1 0.5 0.26 6 WYM84 69860.1 0.5 0.02 14WYM11 69642.2 0.5 0.18 9 WYM84 69865.2 0.5 0.17 9 LNU74_H109 69485.3 0.50.18 8 WYM11 69639.9 0.5 0.01 14 CONT. — 0.4 — — WYM99 70020.3 0.5 L 16WYM99 70016.3 0.4 0.02 12 WYM11 69640.3 0.4 0.07 8 WYM101 69712.3 0.40.16 7 WYM109 69717.3 0.5 L 17 WYM84 69862.1 0.4 0.25 6 WYM108 69634.10.4 0.01 11 WYM84 69864.5 0.4 L 12 CONT. — 0.4 — — WYM100 69873.2 0.50.18 10 CONT. — 0.5 — — WYM101 69715.8 0.5 0.17 9 WYM108 69632.1 0.50.16 11 WYM108 69636.6 0.5 0.11 9 WYM4 69737.8 0.5 0.19 10 WYM11 69640.10.5 L 16 CONT. — 0.4 — — WYM100 69872.5 0.5 0.13 11 WYM13 69645.2 0.50.10 14 WYM99 70016.8 0.5 0.23 9 CONT. — 0.5 — — LNU74_H109 69483.3 0.50.16 9 CONT. — 0.5 — — WYM99 70017.5 0.5 0.19 7 WYM13 69647.7 0.5 0.23 7CONT. — 0.4 — — WYM11 69641.2 0.5 0.22 6 WYM98 70009.2 0.5 0.16 7LNU74_H109 69483.4 0.5 0.02 13 CONT. — 0.4 — — WYM4 69739.2 0.4 0.05 10LNU74_H109 69482.1 0.4 0.06 10 WYM100 69874.5 0.4 0.23 6 WYM99 70020.10.4 0.26 6 CONT. — 0.4 — — WYM13 69647.4 0.5 0.07 10 WYM109 69719.2 0.5L 15 WYM11 69638.1 0.5 0.27 7 WYM84 69864.1 0.5 0.26 8 CONT. — 0.4 — —WYM99 70017.4 0.4 0.16 11 CONT. — 0.4 — — Table 57. “CONT.” - Control;“Ave.” - Average; “% Incr.” = % increment; “p-val.” - p-value, L - p <0.01.

TABLE 58 Genes showing improved plant performance at normal growthconditions under regulation of At6669 promoter Rosette Rosette HarvestIndex Area [cm²] Diameter [cm] P- % P- % P- % Gene Name Event # Ave.Val. Incr. Ave. Val. Incr. Ave. Val. Incr. WYM7 71168.1 0.3 0.07 14 9.60.07 17 5.5 0.05 11 WYM17 71315.1 — — — 9.1 0.05 11 5.4 0.03 8 WYM10671687.6 — — — 9.1 0.02 10 5.3 L 7 WYM110 71443.5 — — — — — — 5.1 0.09 2WYM52 71461.2 0.3 0.10 9 8.6 0.21 4 5.3 0.04 6 WYM106 71685.3 0.3 0.09 89.9 0.02 20 5.5 0.03 11 CONT. — 0.3 — — 8.2 — — 5.0 — — WYM47 69683.5 —— — 8.7 0.03 12 5.1 0.05 7 WYM7 71172.5 — — — — — — 5.0 0.18 4 CONT. —0.3 — — 7.7 — — 4.8 — — WYM26 71627.6 — — — 8.1 0.15 10 4.9 0.29 3 WYM7770949.3 0.3 0.17 13 — — — — — — WYM77 70947.2 — — — 7.7 0.26 5 — — —WYM17 71314.3 — — — 7.6 0.27 4 — — — CONT. — 0.2 — — 7.4 — — 4.7 — —WYM7 71172.1 0.3 0.24 10 — — — — — — WYM7 71169.7 — — — 11.6 0.22 9 6.00.28 4 WYM7 71170.1 0.3 0.22 9 — — — — — — WYM95 70181.2 0.3 0.14 1511.7 0.21 10 6.1 0.22 5 CONT. — 0.3 — — 10.7 — — 5.7 — — WYM80 69993.20.3 0.06 20 — — — — — — WYM95 70182.3 — — — 7.5 0.27 6 4.7 0.24 3 WYM1771313.9 0.3 0.09 20 — — — 4.7 0.20 3 WYM95 70182.5 0.3 0.08 9 — — — 4.70.23 2 WYM47 69685.5 — — — 7.4 0.27 4 4.7 0.22 3 WYM17 71316.2 0.3 L 22— — — — — — WYM95 70178.1 0.3 0.09 8 — — — — — — CONT. — 0.2 — — 7.1 — —4.6 — — WYM106 71684.4 — — — 7.4 0.18 9 4.6 0.21 4 WYM110 71442.5 — — —8.9 L 32 5.2 0.02 16 WYM47 69681.4 — — — 8.1 0.08 20 4.9 0.04 11 WYM2671627.4 — — — 7.4 0.21 9 4.7 0.20 5 WYM26 71626.6 — — — 7.4 0.22 9 4.70.20 5 WYM110 71445.5 — — — 7.3 0.25 7 4.8 0.13 7 WYM106 71687.1 — — —7.4 0.15 9 4.8 0.07 7 CONT. — 0.3 — — 6.8 — — 4.5 — — WYM52 71463.4 0.30.15 17 9.5 0.08 20 5.5 0.08 10 WYM110 71445.6 0.3 0.02 35 9.1 0.05 155.3 0.10 7 WYM44 71321.3 0.3 0.05 24 9.8 0.02 25 5.7 0.02 14 WYM7770948.2 0.3 0.04 30 9.9 0.04 25 5.6 0.04 12 WYM26 71623.2 0.3 0.01 2510.1 L 28 5.6 0.02 13 WYM80 69994.2 0.3 L 30 10.8 L 37 5.8 0.01 17WYM110 71443.6 0.3 0.03 35 9.0 0.09 14 5.3 0.10 7 WYM17 71313.6 0.3 0.0239 9.4 0.03 19 5.4 0.07 9 CONT. — 0.2 — — 7.9 — — 5.0 — — WYM95 70181.10.3 0.07 23 — — — — — — WYM47 69685.1 0.3 0.01 34 8.4 0.15 13 5.1 0.17 7WYM95 70183.2 0.3 0.16 13 8.1 0.19 9 5.0 0.19 2 WYM47 69683.3 0.3 0.0423 8.3 0.16 11 5.1 0.14 8 WYM95 70181.3 0.3 0.09 19 — — — — — — WYM8069994.4 — — — 8.9 0.07 20 5.1 0.18 7 WYM26 71622.3 0.3 0.16 11 8.4 0.1213 5.0 0.18 5 CONT. — 0.2 — — 7.4 — — 4.7 — — WYM26 71626.1 — — — 10.00.17 8 5.5 0.11 4 WYM52 71465.5 — — — 10.7 0.06 16 5.6 0.09 6 WYM10671685.5 0.3 0.22 8 — — — — — — CONT. — 0.3 — — 9.2 — — 5.3 — — WYM771169.2 — — — 10.6 0.05 18 5.7 0.04 12 WYM52 71461.6 0.3 0.18 21 — — —5.3 0.25 4 CONT. — 0.3 — — 9.0 — — 5.1 — — WYM26 71626.2 — — — 9.3 0.256 5.2 0.30 2 WYM17 71315.4 — — — 9.3 0.25 7 — — — CONT. — 0.3 — — 8.7 —— 5.1 — — WYM7 71170.5 — — — 9.1 0.25 8 5.4 0.12 8 WYM7 71170.3 0.3 0.2412 9.5 0.16 12 5.3 0.13 8 WYM106 71685.6 — — — — — — 5.1 0.27 4 WYM5271463.6 — — — 10.0 0.21 17 5.4 0.21 9 CONT. — 0.3 — — 8.5 — — 5.0 — —WYM52 71461.5 0.3 0.29 3 9.0 0.18 13 5.2 0.15 7 WYM106 71687.3 — — — 9.80.02 23 5.4 0.03 11 WYM52 71465.2 0.4 0.02 17 8.7 0.09 10 5.2 0.06 8WYM7 71170.2 — — — 8.7 0.28 9 5.2 0.20 8 WYM110 71445.1 — — — 9.7 L 225.4 0.03 11 WYM52 71465.4 — — — 9.1 0.03 15 5.3 0.05 9 WYM44 71321.5 0.40.07 16 11.1 L 39 5.8 L 20 WYM44 71317.8 0.3 0.10 9 9.0 0.06 13 5.2 0.059 CONT. — 0.3 — — 7.9 — — 4.8 — — WYM44 71322.6 0.3 0.14 11 — — — 5.50.18 6 WYM26 71626.4 0.3 0.08 15 10.6 0.06 14 5.5 0.07 6 WYM7 71169.50.3 0.11 13 — — — — — — WYM47 69684.3 0.3 0.03 24 10.4 0.13 12 5.6 0.048 WYM110 71445.2 0.3 0.29 5 — — — — — — WYM110 71442.2 0.3 0.27 7 — — —— — — CONT. — 0.3 — — 9.3 — — 5.2 — — WYM92 70001.1 — — — 9.0 0.11 155.1 0.10 8 WYM60 69869.3 — — — 8.4 0.25 8 — — — CONT. — 0.3 — — 7.8 — —4.8 — — WYM37 70944.7 0.3 0.29 2 9.4 0.02 21 5.2 0.04 8 WYM57 69512.70.4 0.01 9 8.8 0.06 13 5.0 0.12 5 WYM37 70942.4 — — — 9.5 0.02 23 5.20.06 10 WYM27 69935.2 0.4 0.09 13 8.8 0.10 13 5.0 0.17 5 WYM58 69959.30.3 0.28 4 8.4 0.17 8 — — — WYM63 69984.2 0.3 0.27 5 8.8 0.08 14 5.00.09 6 WYM60 69870.2 0.4 0.09 11 8.5 0.26 10 — — — CONT. — 0.3 — — 7.8 —— 4.8 — — WYM63 69982.4 0.4 0.30 4 10.9 L 33 6.0 L 20 WYM27 69936.2 — —— 9.4 L 16 5.4 0.03 9 WYM51 69954.2 — — — 9.8 0.02 20 5.3 L 8 WYM9270003.1 — — — 9.9 0.01 21 5.4 0.02 9 LYM90 69389.5 — — — 10.1 L 24 5.5 L10 WYM60 69870.8 — — — 10.1 L 24 5.5 0.01 10 WYM51 69950.5 — — — 9.20.05 13 5.4 0.07 8 WYM27 69937.5 — — — 9.1 0.02 11 5.3 0.02 7 CONT. —0.3 — — 8.2 — — 5.0 — — WYM60 69869.2 0.3 L 30 — — — — — — WYM58 69960.20.3 0.20 9 — — — — — — WYM51 69950.1 0.3 0.04 22 10.2 0.03 20 5.4 0.05 8WYM92 70000.5 0.3 L 18 — — — — — — WYM58 69961.10 0.3 L 27 — — — — — —WYM63 69983.2 0.3 L 29 — — — — — — WYM37 70944.8 0.3 0.05 17 — — — — — —WYM63 69980.3 0.3 L 21 — — — — — — CONT. — 0.2 — — 8.5 — — 5.0 — — WYM9269998.2 — — — 8.1 0.09 10 4.7 0.11 3 WYM63 69982.1 — — — 8.9 L 20 5.10.01 10 WYM37 70942.3 — — — — — — 4.8 0.07 5 WYM63 69984.6 — — — 7.80.25 6 4.7 0.18 2 WYM60 69868.3 — — — 8.4 0.03 14 4.9 0.03 7 WYM6670175.3 — — — 8.3 0.17 12 4.8 0.19 6 CONT. — 0.3 — — 7.4 — — 4.6 — —WYM37 70942.6 0.4 0.05 15 11.4 0.03 27 6.0 0.04 15 WYM57 69514.2 — — —12.8 L 43 6.3 L 21 WYM66 70176.2 0.3 0.26 4 11.7 0.01 30 5.9 0.01 14WYM92 70000.3 0.4 0.10 13 12.1 L 35 6.2 L 20 WYM60 69867.2 0.4 0.04 1712.7 L 41 6.2 L 19 WYM60 69870.3 0.4 0.05 15 10.7 0.06 19 5.8 0.05 11WYM66 70174.1 — — — 10.1 0.10 13 5.6 0.07 8 CONT. — 0.3 — — 9.0 — — 5.2— — WYM57 69517.1 — — — 11.6 L 30 6.0 L 15 WYM60 69868.5 — — — 11.8 0.0232 6.1 0.01 16 WYM58 69961.9 — — — 11.0 L 23 5.7 0.03 10 WYM27 69935.90.4 0.03 17 11.0 0.01 24 5.8 0.04 11 WYM66 70174.4 0.3 0.27 4 11.8 0.0233 6.0 0.03 16 WYM33 69942.2 0.3 0.12 8 10.5 L 18 5.8 L 11 WYM33 69942.1— — — 11.5 0.01 29 5.9 0.02 14 WYM57 69515.4 — — — 13.5 L 52 6.3 L 21CONT. — 0.3 — — 8.9 — — 5.2 — — WYM57 69514.3 0.3 0.25 8 9.1 0.15 16 5.20.16 7 WYM57 69513.3 — — — 9.6 0.02 22 5.4 0.02 12 LYM90 69388.2 0.30.15 9 9.4 0.07 19 5.3 0.06 9 WYM60 69867.3 0.3 0.03 23 9.3 0.07 18 5.30.04 10 WYM27 69937.1 0.3 0.11 14 8.3 0.29 6 5.0 0.25 4 LYM90 69389.60.3 0.14 10 — — — — — — WYM37 70939.4 0.3 0.08 14 — — — — — — CONT. —0.2 — — 7.9 — — 4.8 — — WYM37 70942.5 0.3 0.27 5 10.9 L 25 5.7 L 10WYM33 69938.6 — — — 9.2 0.27 4 — — — WYM58 69960.7 0.3 0.22 9 10.4 0.0419 5.6 0.02 7 WYM57 69515.1 0.3 0.28 6 9.8 0.09 12 5.4 0.19 4 WYM2769935.4 — — — 9.3 0.29 6 — — — CONT. — 0.3 — — 8.8 — — 5.2 — — WYM6670174.3 0.3 0.16 6 9.8 0.23 6 5.5 0.16 5 WYM92 69999.3 0.3 0.17 6 — — —— — — WYM33 69943.2 0.3 0.07 13 — — — — — — LYM90 69388.5 — — — 11.00.02 18 5.8 0.03 10 WYM58 69960.3 0.3 0.23 5 — — — — — — WYM51 69950.30.3 0.19 9 9.9 0.22 6 — — — CONT. — 0.3 — — 9.3 — — 5.3 — — LYM9069386.3 0.4 0.03 14 10.3 0.13 10 5.7 0.09 9 WYM27 69936.1 0.4 0.14 9 — —— 5.6 0.11 7 LYM90 69388.4 0.4 0.17 8 10.2 0.16 9 5.7 0.06 8 WYM3369939.1 0.4 0.14 7 — — — 5.5 0.29 4 WYM57 69512.2 0.4 0.06 12 — — — — —— WYM66 70175.4 0.4 0.02 17 10.1 0.27 7 5.7 0.16 9 CONT. — 0.4 — — 9.4 —— 5.3 — — WYM60 69870.5 — — — 10.6 0.15 9 5.8 0.14 5 WYM58 69961.3 — — —10.2 0.27 5 — — — CONT. — 0.4 — — 9.7 — — 5.5 — — WYM51 69953.5 0.3 0.2010 — — — — — — WYM58 69961.7 0.3 0.17 4 9.0 0.18 8 5.2 0.12 5 WYM9270000.4 0.3 0.26 2 8.6 0.26 4 5.1 0.18 3 WYM51 69954.7 0.3 0.22 6 9.50.04 14 5.2 0.08 6 WYM57 69513.2 — — — — — — 5.2 0.11 5 WYM66 70175.20.3 0.23 9 9.2 0.05 10 5.3 0.03 8 WYM66 70173.1 — — — 9.8 0.02 18 5.40.04 10 CONT. — 0.3 — — 8.3 — — 4.9 — — WYM108 69633.1 — — — 7.4 0.15 94.9 0.02 7 WYM13 69646.1 — — — 9.0 L 33 5.3 L 16 WYM98 70008.2 0.3 0.226 7.6 0.03 11 5.0 0.05 9 LNU74_H109 69484.1 — — — 7.7 0.02 13 4.9 0.01 6WYM99 70020.4 — — — 7.7 0.12 13 4.8 0.13 6 WYM109 69717.2 0.3 0.20 9 — —— — — — CONT. — 0.2 — — 6.8 — — 4.6 — — WYM108 69635.1 — — — 7.7 0.15 95.0 0.14 5 WYM84 69860.1 — — — 8.4 0.02 18 5.2 0.03 11 WYM11 69642.2 — —— 7.7 0.14 9 5.0 0.14 5 WYM84 69865.2 — — — 8.3 0.05 17 5.2 0.04 10LNU74_H109 69485.3 — — — 7.4 0.27 5 5.0 0.16 5 WYM11 69639.9 — — — 9.7 L37 5.6 L 17 CONT. — 0.3 — — 7.1 — — 4.7 — — WYM99 70020.3 0.2 0.15 107.3 L 17 4.8 L 9 WYM99 70016.3 0.3 0.03 17 7.2 0.02 15 4.8 0.01 9 WYM1169640.3 0.2 0.20 6 6.6 0.10 6 4.5 0.07 4 WYM101 69712.3 — — — — — — 4.50.20 3 WYM109 69717.3 0.2 0.26 5 7.7 0.04 24 5.0 0.03 14 WYM84 69862.1 —— — — — — 4.5 0.25 2 WYM108 69634.1 0.2 0.12 9 7.3 L 17 4.8 L 10 WYM8469864.5 0.2 0.13 10 6.8 0.02 8 4.7 0.01 7 CONT. — 0.2 — — 6.2 — — 4.4 —— WYM11 69641.3 — — — 9.9 0.02 11 5.6 0.07 6 WYM98 70009.1 — — — 9.50.16 6 5.4 0.30 2 WYM4 69737.3 — — — 9.3 0.20 4 — — — LNU74_H109 69487.1— — — 9.4 0.15 5 5.4 0.22 3 WYM100 69873.2 — — — 10.3 0.11 15 5.7 0.12 7WYM101 69713.5 — — — 9.3 0.30 4 — — — WYM109 69720.8 — — — 9.5 0.19 6 —— — WYM99 70016.10 — — — 9.4 0.25 5 5.5 0.29 3 CONT. — 0.3 — — 8.9 — —5.3 — — WYM109 69720.7 — — — 8.0 0.25 7 — — — WYM100 69875.4 0.3 0.14 9— — — — — — WYM101 69715.8 0.3 0.10 11 8.5 0.09 13 5.1 0.09 6 WYM10869632.1 — — — 9.5 0.08 27 5.4 0.06 13 WYM108 69636.6 0.3 0.28 5 8.5 0.0314 5.2 0.03 8 WYM4 69737.8 0.3 0.08 13 8.4 0.12 12 5.2 0.16 7 WYM1169640.1 — — — 9.4 0.02 26 5.4 L 12 CONT. — 0.3 — — 7.5 — — 4.8 — — WYM469734.2 0.3 0.24 8 — — — — — — WYM4 69736.3 0.3 0.28 8 9.7 0.14 11 5.40.21 4 WYM100 69872.5 0.3 0.29 6 10.5 0.02 21 5.6 0.04 8 WYM13 69645.2 —— — 10.8 0.01 24 6.0 L 15 WYM99 70016.8 0.3 0.09 11 10.4 0.03 19 5.60.04 7 WYM109 69716.3 0.3 0.09 20 — — — — — — CONT. — 0.3 — — 8.7 — —5.2 — — WYM109 69716.1 0.3 0.07 23 9.4 0.16 9 5.4 0.21 4 WYM4 69735.30.3 0.07 18 — — — — — — WYM101 69710.2 0.3 0.24 9 9.7 0.05 13 5.5 0.10 5LNU74_H109 69483.3 0.3 0.15 11 10.2 0.02 19 5.8 0.02 10 WYM108 69636.50.3 0.05 19 9.5 0.23 11 5.5 0.20 6 WYM101 69712.2 0.3 0.19 9 9.5 0.08 105.4 0.15 4 WYM98 70008.3 0.3 0.07 19 9.4 0.20 10 5.5 0.18 5 CONT. — 0.2— — 8.6 — — 5.2 — — WYM109 69716.4 0.3 0.16 8 — — — 5.2 0.24 4 WYM1169640.7 — — — — — — 5.2 0.18 3 WYM11 69641.1 0.3 0.02 13 8.8 0.02 11 5.20.08 4 WYM99 70017.5 — — — — — — 5.1 0.24 2 WYM98 70009.3 — — — 8.6 0.049 5.4 0.02 7 CONT. — 0.2 — — 7.9 — — 5.0 — — WYM84 69860.6 0.3 0.09 13 —— — — — — WYM13 69647.9 0.2 0.27 4 8.0 0.09 4 — — — WYM100 69875.3 0.20.15 8 — — — — — — WYM13 69644.2 0.2 0.22 5 8.0 0.17 5 5.2 0.13 3 WYM9870008.1 0.3 0.05 13 8.1 0.19 5 5.3 0.08 5 WYM101 69715.5 — — — 8.6 0.0212 5.3 0.03 6 WYM84 69864.2 0.2 0.06 10 8.3 0.17 8 5.2 0.10 4 WYM9870005.3 0.3 0.02 13 8.1 0.03 6 5.1 0.27 2 CONT. — 0.2 — — 7.7 — — 5.0 —— WYM100 69874.1 0.3 0.10 17 — — — 4.9 0.14 2 WYM11 69641.2 0.3 0.17 7 —— — 4.9 0.10 3 WYM98 70005.2 0.3 0.03 15 — — — 4.8 0.24 2 WYM98 70009.60.3 0.14 7 — — — 4.8 0.28 1 WYM4 69737.5 0.3 0.12 6 — — — — — —LNU74_H109 69483.4 0.3 0.04 17 9.2 0.04 23 5.3 0.03 12 CONT. — 0.2 — —7.5 — — 4.8 — — WYM4 69739.2 0.3 0.02 16 6.8 L 16 4.7 L 8 LNU74_H10969482.1 0.3 0.01 23 7.4 L 26 4.7 0.03 9 LNU74_H109 69482.2 0.3 0.03 176.6 0.05 13 4.4 0.22 2 WYM108 69635.3 0.2 0.30 6 6.3 0.15 7 4.4 0.18 2WYM100 69874.5 0.3 0.01 16 6.7 0.01 14 4.5 0.04 5 WYM98 70008.4 0.3 0.1316 6.2 0.26 6 — — — WYM99 70020.1 0.3 0.06 13 6.8 L 16 4.6 0.02 6 CONT.— 0.2 — — 5.9 — — 4.3 — — WYM108 69634.2 0.2 0.12 8 — — — — — — WYM8469860.2 0.3 0.03 12 — — — — — — WYM13 69645.5 0.3 L 22 7.6 0.18 8 4.80.20 4 WYM13 69647.1 0.3 L 20 — — — — — — WYM4 69737.1 0.2 0.23 8 — — —— — — CONT. — 0.2 — — 7.1 — — 4.6 — — WYM99 70016.9 — — — 7.5 0.25 8 — —— WYM13 69647.4 — — — 8.5 L 22 5.3 0.01 10 WYM109 69719.2 0.3 0.05 128.7 0.01 25 5.3 L 11 WYM101 69715.2 0.3 0.17 5 8.0 0.07 15 5.0 0.13 4WYM11 69638.1 0.3 0.07 10 8.2 0.05 17 5.1 0.08 7 WYM99 70016.2 0.3 0.303 7.4 0.20 6 — — — WYM84 69864.1 — — — 8.6 0.05 24 5.2 0.04 9 CONT. —0.3 — — 7.0 — — 4.8 — — LNU74_H109 69483.5 — — — 7.4 0.28 5 4.7 0.15 2WYM101 69715.1 0.3 0.07 11 — — — — — — WYM99 70017.4 — — — 8.8 0.06 245.2 0.03 13 WYM108 69635.2 0.3 0.20 8 — — — — — — WYM109 69718.2 0.30.10 9 — — — 4.8 0.17 4 CONT. — 0.3 — — 7.1 — — 4.6 — — Table 58.“CONT.” - Control; “Ave.” - Average; “% Incr” = % increment; “p-val.” -p-value, L - p < 0.01.

TABLE 59 Genes showing improved plant performance at normal growthconditions under regulation of At6669 promoter Seed Yield [mg] 1000 SeedWeight [mg] Gene Name Event # Ave. P-Val. % Incr. Ave. P-Val. % Incr.WYM7 71169.2 — — — 25.6 L 43 WYM52 71461.6 266.5 0.13 28 18.7 0.22 4WYM95 70181.6 — — — 18.5 0.28 4 CONT. — 208.8 — — 17.9 — — WYM47 69684.1— — — 21.3 0.20 9 WYM17 71315.4 — — — 22.3 0.02 14 CONT. — 240.5 — —19.5 — — WYM52 71465.5 — — — 21.4 L 14 CONT. — 213.9 — — 18.8 — — WYM5271463.4 186.2 0.23 19 19.2 0.28 4 WYM110 71445.6 183.8 0.14 18 — — —WYM44 71321.3 198.0 0.04 27 — — — WYM77 70948.2 208.0 0.05 33 — — —WYM26 71623.2 212.5 0.01 36 — — — WYM80 69994.2 218.8 0.04 40 — — —WYM110 71443.6 221.4 0.06 42 18.9 0.12 2 WYM17 71313.6 193.9 0.14 24 — —— CONT. — 156.4 — — 18.5 — — WYM110 71443.5 — — — 18.8 0.10 7 WYM5271461.2 183.1 0.25 8 — — — WYM77 70947.1 — — — 22.3 L 26 WYM7 71168.1184.7 0.19 8 — — — WYM106 71685.3 197.1 0.03 16 — — — CONT. — 170.3 — —17.7 — — WYM47 69685.1 220.5 0.02 43 — — — WYM95 70181.1 180.8 0.18 17 —— — WYM95 70183.2 194.3 0.07 26 23.3 0.03 18 WYM47 69683.3 193.2 0.04 25— — — WYM80 69994.4 — — — 21.6 0.13 10 WYM95 70181.3 178.6 0.14 16 — — —WYM26 71622.3 199.0 0.03 29 21.5 0.10 9 WYM77 70949.1 167.7 0.24 9 — — —CONT. — 154.5 — — 19.8 — — WYM47 69682.4 — — — 31.1 L 62 WYM47 69683.5 —— — 20.9 0.15 9 CONT. — 185.7 — — 19.2 — — WYM26 71627.6 — — — 22.4 L 17WYM77 70949.3 187.4 0.02 20 — — — WYM110 71443.1 164.5 0.26 5 — — —WYM106 71685.2 166.0 0.28 6 19.8 0.17 4 CONT. — 155.9 — — 19.0 — — WYM9570182.5 182.0 0.04 24 — — — WYM17 71316.2 165.5 0.07 13 — — — WYM4769685.5 169.9 0.21 16 — — — WYM26 71623.1 — — — 20.0 0.12 9 WYM9570178.1 173.8 0.06 19 — — — WYM80 69993.2 204.3 0.04 40 — — — WYM9570182.3 152.0 0.21 4 — — — WYM17 71313.9 193.5 0.08 32 — — — CONT. —146.2 — — 18.4 — — WYM110 71442.5 — — — 20.6 0.02 9 CONT. — 178.8 — —18.9 — — WYM52 71463.6 271.3 0.27 16 — — — WYM106 71685.6 — — — 20.10.08 8 WYM80 69994.3 — — — 19.4 0.24 5 WYM17 71314.4 — — — 22.0 0.19 19CONT. — 233.2 — — 18.5 — — WYM52 71465.2 270.0 0.04 16 — — — WYM5271465.4 247.3 0.18 7 — — — WYM110 71445.1 — — — 20.5 0.03 10 WYM4471321.5 279.9 0.07 21 — — — WYM44 71317.8 249.4 0.17 8 — — — CONT. —231.9 — — 18.7 — — WYM95 70181.2 245.9 0.21 14 — — — WYM17 71315.2 — — —21.9 0.05 12 CONT. — 215.5 — — 19.5 — — WYM26 71626.4 278.2 0.06 27 — —— WYM47 69684.3 267.9 0.13 22 — — — WYM77 70948.4 — — — 30.6 L 59 CONT.— 218.9 — — 19.3 — — WYM13 69646.1 — — — 21.6 L 17 WYM98 70008.2 168.70.07 9 19.3 0.16 5 LNU74_H109 69484.1 166.9 0.22 8 19.9 0.03 8 WYM9970020.4 164.9 0.23 6 — — — WYM109 69717.2 163.3 0.30 5 — — — WYM10869633.1 169.5 0.29 9 19.9 0.13 8 WYM4 69736.6 160.9 0.24 4 — — — CONT. —155.2 — — 18.4 — — WYM13 69645.2 — — — 22.7 0.04 10 WYM99 70016.8 214.10.22 8 — — — WYM109 69716.3 238.0 0.17 20 — — — WYM100 69872.5 219.10.17 11 — — — CONT. — 197.7 — — 20.6 — — WYM98 70005.2 181.7 0.15 7 — —— WYM4 69737.5 — — — 19.5 0.03 3 LNU74_H109 69483.4 205.1 0.07 21 21.10.03 12 CONT. — 169.3 — — 18.9 — — WYM4 69739.2 174.8 0.12 13 — — —LNU74_H109 69482.1 195.7 0.01 27 — — — LNU74_H109 69482.2 179.0 0.03 16— — — WYM100 69874.5 182.4 0.06 18 — — — WYM498 70008.4 168.6 0.24 9 — —— WYM499 70020.1 169.1 0.11 10 — — — CONT. — 154.4 — — 18.9 — — WY1419970016.3 171.5 0.20 8 — — — WYM109 69717.3 — — — 20.4 0.16 7 WYM8469864.5 167.8 0.23 6 — — — CONT. — 158.1 — — 19.1 — — WYM108 69634.2 — —— 19.5 0.24 5 WYM84 69860.2 171.4 0.10 17 — — — WYM13 69645.5 185.5 0.0221 — — — WYM13 69647.1 197.9 L 29 — — — CONT. — 152.9 — — 18.6 — —LNU74_H109 69483.5 — — — 22.2 L 14 WYM499 70017.4 — — — 21.0 0.06 0.06LNU74_H109 69485.2 — — — 21.4 0.07 10 CONT. — 189.6 — — 19.4 — — WYM1169638.1 202.2 0.2.3 9 27.0 0.28 21 WYM99 70016.9 198.3 0.30 7 — — —WYM109 69719.2 210.1 0.15 13 — — — CONT. — 185.9 — — 22.2 — — WYM10169715.3 191.0 0.29 11 — — — WYM11 69642.2 184.9 0.29 7 — — — WYM1169639.9 — — — 22.1 L 14 WYM84 69860.1 — — — 22.0 L 14 CONT. — 172.5 — —19.4 — — WYM13 69644.2 160.0 0.13 7 — — — WYM98 70008.1 162.6 0.05 9 — —— WYM101 69715.5 163.8 0.12 10 22.6 L 14 WYM84 69864.2 164.5 0.09 10 — —— WYM98 70005.3 164.7 0.10 10 — — — WYM84 69860.6 172.4 0.08 16 — — —WYM13 69647.9 162.4 0.06 9 — — — WYM100 69875.3 163.2 0.12 9 — — — CONT.— 149.1 — — 19.8 — — WYM98 70008.3 178.4 0.15 13 — — — WYM109 69716.1177.6 0.22 13 — — — WYM4 69735.3 183.3 0.10 17 — — — WYM101 69710.2189.1 0.06 20 — — — LNU74_H109 69483.3 196.5 0.06 25 21.8 0.05 14 WYM10869636.5 189.3 0.07 20 — — — WYM101 69712.2 171.9 0.24 9 19.5 0.21 2CONT. — 157.2 — — 19.2 — — WYM109 69716.4 182.2 0.24 5 — — — WYM9870009.3 — — — 22.0 0.11 9 WYM11 69641.1 186.4 0.06 8 — — — WYM19970017.5 — — — 30.6 L 51 CONT. — 172.8 — — 20.3 — — WYM99 70016.10 — — —22.2 L 18 CONT. — 242.4 — — 18.9 — — WYM109 69720.7 — — — 20.6 0.04 8WYM101 69715.8 191.4 0.18 9 — — — WYM108 69636.6 189.6 0.17 8 — — — WYM469737.8 191.0 0.15 8 — — — CONT. — 176.3 — — 19.2 — — WYM37 70942.5206.7 0.04 15 18.5 0.02 6 WYM57 69515.1 190.9 0.27 6 — — — WYM27 69935.4195.4 0.14 9 18.7 L 7 WYM58 69960.7 200.9 0.12 12 — — — WYM57 69513.8 —— — 17.8 0.25 2 CONT. — 179.7 — — 17.5 — — WYM37 70944.8 180.4 0.10 15 —— — WYM63 69980.3 175.8 0.08 12 — — — WYM92 70000.5 187.2 0.02 20 21.6 L20 WYM58 69961.10 181.6 0.03 16 — — — WYM63 69983.2 187.5 0.03 20 — — —WYM60 69869.2 183.5 0.03 17 — — — WYM58 69960.2 176.2 0.08 13 19.5 L 8WYM51 69950.1 194.0 L 24 20.3 0.02 12 CONT. — 156.5 — — 18.1 — — WYM6369982.1 — — — 17.9 0.19 2 CONT. — 178.6 — — 17.5 — — LYM90 69388.2 175.00.06 16 18.1 0.30 3 WYM60 69867.3 197.1 0.01 31 — — — WYM27 69937.1170.1 0.15 13 — — — LYM90 69389.6 169.2 0.16 17 — — — WYM37 70939.4178.4 0.08 18 — — — WYM57 69514.3 173.2 0.20 15 — — — WYM57 69513.3172.4 0.14 14 19.0 0.09 8 CONT. — 151.0 — — 17.7 — — WYM51 69954.7 — — —18.7 0.06 4 WYM37 70944.2 176.7 0.17 6 — — — CONT. — 166.6 — — 18.0 — —WYM60 69870.2 197.2 0.21 8 — — — WYM57 69512.7 197.0 0.05 8 — — — WYM2769935.2 206.3 0.16 13 — — — CONT. — 182.3 — — 18.2 — — WYM37 70942.6253.7 0.04 29 — — — WYM57 69514.2 216.5 0.17 10 21.0 0.05 12 WYM6670176.2 224.2 0.11 14 — — — WYM92 70000.3 236.2 0.09 21 — — — WYM6069867.2 281.5 0.02 44 19.2 0.13 3 WYM60 69870.3 229.0 0.12 17 — — —CONT. — 196.0 — — 18.7 — — WYM57 69515.4 — — — 19.0 0.08 6 WYM33 69942.1210.6 0.01 18 20.5 0.05 14 WYM57 69517.1 — — — 21.9 L 22 WYM60 69868.5197.9 0.04 11 — — — WYM27 69935.9 217.9 0.03 22 — — — WYM66 70174.4191.8 0.28 8 — — — WYM33 69942.2 209.4 0.07 18 18.9 0.06 5 CONT. — 178.0— — 18.0 — — WYM63 69982.4 191.5 0.06 7 — — — WYM92 70003.1 184.7 0.21 3— — — WYM60 69870.8 — — — 18.8 0.17 3 CONT. — 179.1 — — 18.2 — — LYM9069386.3 258.2 0.01 15 — — — WYM27 69936.1 241.9 0.22 8 19.2 0.17 8 LYM9069388.4 239.7 0.21 7 18.4 0.26 4 WYM33 69939.1 242.6 0.13 8 19.7 0.04 10WYM57 69512.2 258.7 0.12 16 — — — WYM66 70175.4 273.9 L 22 — — — CONT. —223.7 — — 17.8 — — WYM60 69869.3 — — — 21.9 0.03 16 CONT. — 178.6 — —18.9 — — WYM60 69870.5 — — — 20.9 0.05 11 WYM58 69960.1 — — — 20.6 0.0210 CONT. — 225.9 — — 18.8 — — WYM33 69943.2 198.2 0.21 8 — — — LYM9069388.5 — — — 21.5 0.02 18 WYM51 69950.3 189.4 0.29 3 — — — CONT. —183.9 — — 18.2 — — LYM90 69389.3 197.1 0.25 5 — — — WYM66 70177.7 — — —18.1 0.28 2 CONT. — 188.3 — — 17.8 — — Table 59. “CONT.” - Control;“Ave.” - Average; “% Incr” = % increment; “p. val.” - p-value, L - p <0.01.

Example 19 Evaluation of Transgenic Arabidopsis for Seed Yield and PlantGrowth Rate Under Normal Conditions in Greenhouse Assays Until Bolting(GH-SB Assays)

Assay 2: Plant Performance Improvement Measured Until Bolting Stage:Plant Biomass and Plant Growth Rate Under Normal Greenhouse Conditions(GH-SB Assays)—

This assay follows the plant biomass formation and the rosette areagrowth of plants grown in the greenhouse under normal growth conditions.Transgenic Arabidopsis seeds were sown in agar media supplemented with ½MS medium and a selection agent (Kanamycin). The T2 transgenic seedlingswere then transplanted to 1.7 trays filled with peat and perlite in a1:1 ratio. The trays were irrigated with a solution containing of 6 mMinorganic nitrogen in the form of KNO₃ with 1 mM KH₂PO₄, 1 mM MgSO₄, 2mM CaCl₂) and microelements. All plants were grown in the greenhouseuntil bolting stage. Plant biomass (the above ground tissue) was weightin directly after harvesting the rosette (plant fresh weight [FW]).Following plants were dried in an oven at 50° C. for 48 hours andweighted (plant dry weight [DW]).

Each construct was validated at its T2 generation. Transgenic plantstransformed with a construct conformed by an empty vector carrying the35S promoter and the selectable marker were used as control.

The plants were analyzed for their overall size, growth rate, freshweight and dry matter. Transgenic plants performance was compared tocontrol plants grown in parallel under the same conditions.Mock-transgenic plants expressing the uidA reporter gene (GUS-Intron) orwith no gene at all, under the same promoter were used as control.

The experiment was planned in nested randomized plot distribution. Foreach gene of the invention three to five independent transformationevents were analyzed from each construct.

Digital Imaging—

A laboratory image acquisition system, which consists of a digitalreflex camera (Canon EOS 300D) attached with a 55 mm focal length lens(Canon EF-S series), mounted on a reproduction device (Kaiser RS), whichincludes 4 light units (4×150 Watts light bulb) was used for capturingimages of plant samples.

The image capturing process was repeated every 2 days starting from day1 after transplanting till day 15. Same camera, placed in a custom madeiron mount, was used for capturing images of larger plants sawn in whitetubs in an environmental controlled greenhouse. The tubs were squareshape include 1.7 liter trays. During the capture process, the tubeswere placed beneath the iron mount, while avoiding direct sun light andcasting of shadows.

An image analysis system was used, which consists of a personal desktopcomputer (Intel P4 3.0 GHz processor) and a public domain program—ImageJ1.39 [Java based image processing program which was developed at theU.S. National Institutes of Health and freely available on the internetat Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/]. Imageswere captured in resolution of 10 Mega Pixels (3888×2592 pixels) andstored in a low compression JPEG (Joint Photographic Experts Groupstandard) format. Next, analyzed data was saved to text files andprocessed using the JMP statistical analysis software (SAS institute).

Leaf Analysis—

Using the digital analysis leaves data was and is calculated, includingleaf number, rosette area, rosette diameter, and leaf blade area.

Vegetative Growth Rate:

the relative growth rate (GR) of leaf number (Formula IX, describedabove), rosette area (Formula XIX described above) and plot coverage(Formula XX, described above) were calculated using the indicatedformulas.

Plant Fresh and Dry Weight—

On about day 80 from sowing, the plants were harvested and directlyweight for the determination of the plant fresh weight (FW) and left todry at 50° C. in a drying chamber for about 48 hours before weighting todetermine plant dry weight (DW).

Statistical Analyses—

To identify outperforming genes and constructs, results from theindependent transformation events tested were analyzed separately. Datawas analyzed using Student's t-test and results were consideredsignificant if the p value was less than 0.1. The JMP statisticssoftware package was used (Version 5.2.1, SAS Institute Inc., Cary,N.C., USA).

Experimental Results:

Tables 60-62 summarize the observed phenotypes of transgenic plantsexpressing the genes constructs using the GH-SB Assays.

The genes listed in Tables 60-62 improved plant performance when grownat normal conditions. These genes produced larger plants with a largerphotosynthetic area, biomass (fresh weight, dry weight, leaf number,rosette diameter, and rosette area), and growth rate. The genes werecloned under the regulation of a constitutive At6669 promoter (SEQ IDNO:9405). The evaluation of each gene was performed by testing theperformance of different number of events. Event with p-value<0.1 wasconsidered statistically significant.

TABLE 60 Genes showing improved plant performance at normal growthconditions under regulation of At6669 promoter Dry Weight [mg] FreshWeight [mg] Leaf Number P- % P- % P- % Gene Name Event # Ave. Val. Incr.Ave. Val. Incr. Ave. Val. Incr. LAB259 69401.8 70.0 0.06 17 836.9 0.0118 10.0 0.01 9 WYM18 70938.3 73.4 0.02 22 923.2 L 30 9.7 0.02 6 WYM8670919.5 69.5 0.07 16 — — — 9.4 0.26 2 WYM30 69672.2 74.1 0.05 23 888.7 L25 10.0 0.05 8 WYM83 70956.7 69.2 0.06 15 837.5 0.08 18 9.6 0.11 5 WYM8370953.1 79.2 0.02 32 912.5 0.01 28 10.7 L 16 WYM105 70931.3 63.4 0.26 6776.8 0.28 9 9.5 0.13 3 WYM83 70955.6 — — — — — — 9.6 0.04 4 CONT. —60.0 — — 711.5 — — 9.2 — — WYM48 69972.5 61.9 0.04 26 711.9 0.07 19 9.9L 8 WYM86 70917.3 73.7 0.02 50 861.9 0.04 44 10.0 0.01 10 WYM32 70412.263.0 0.11 28 663.7 0.25 11 — — — LAB259 69400.1 65.0 0.02 32 700.0 0.0717 9.4 0.02 3 WYM30 69668.2 — — — 650.0 0.27 8 — — — LYM91 69394.5 52.80.28 7 — — — — — — CONT. — 49.2 — — 600.6 — — 9.1 — — WYM61 69974.2 80.80.01 31 850.6 0.05 18 — — — WYM83 70951.3 70.0 0.13 14 776.2 0.25 7 — —— WYM86 70918.6 70.9 0.03 15 900.0 L 24 10.1 0.11 6 WYM105 70930.2 69.00.14 12 819.0 0.04 13 — — — WYM32 70415.2 72.1 0.04 17 787.5 0.07 9 — —— WYM18 70938.6 80.0 L 30 895.8 L 24 9.8 0.30 2 WYM83 70951.4 82.5 L 34950.0 L 31 10.4 0.10 8 CONT. — 61.6 — — 723.2 — — 9.6 — — WYM86 70919.266.7 0.02 24 758.3 0.03 18 — — — WYM61 69978.1 56.2 0.29 4 710.1 0.03 11— — — WYM87 70960.8 63.1 0.09 17 781.5 L 22 9.7 0.17 4 WYM32 70414.369.5 L 29 809.5 L 26 10.0 0.04 7 WYM32 70413.2 70.9 0.06 32 791.7 0.0123 9.6 0.22 3 WYM83 70956.5 62.1 0.09 15 766.7 0.09 19 — — — WYM3069672.4 68.2 0.14 27 798.8 0.02 24 10.0 0.04 7 LYM91 69395.2 58.8 0.06 9834.5 0.02 30 — — — CONT. — 53.9 — — 641.7 — — 9.3 — — WYM18 70938.787.5 0.19 12 1179.2 0.07 15 10.9 0.03 8 WYM87 70960.3 — — — 1091.7 0.177 — — — WYM32 70416.3 — — — — — — 11.0 0.06 9 CONT. — 77.9 — — 1025.0 —— 10.1 — — WYM105 70932.10 60.7 0.07 20 617.9 0.07 14 — — — WYM10570932.9 56.3 0.16 12 608.3 0.09 12 — — — LYM91 69395.1 — — — 583.3 0.288 — — — WYM87 70961.7 54.4 0.07 8 605.6 0.10 12 — — — WYM105 70930.157.5 0.06 14 616.7 0.07 14 — — — WYM30 69672.1 — — — 591.7 0.16 9 — — —LAB259 69401.1 61.3 0.03 21 650.0 0.03 20 — — — CONT. — 50.5 — — 541.5 —— 9.8 — — WYM32 70417.1 66.7 L 13 804.2 L 11 9.8 L 8 WYM61 69978.3 — — —748.4 0.22 4 9.4 0.23 4 WYM86 70919.1 — — — — — — 9.3 0.10 3 WYM8370953.2 65.7 0.19 12 — — — 9.7 0.09 7 WYM83 70956.1 62.7 0.27 7 774.40.03 7 9.3 L 3 WYM86 70920.1 67.5 L 15 856.9 0.01 19 9.5 0.06 5 CONT. —58.9 — — 721.4 — — 9.0 — — WYM48 69972.3 71.3 0.04 15 912.5 0.13 8 10.00.26 3 LYM91 69392.6 75.2 0.08 21 952.4 0.13 13 — — — WYM18 70936.3 67.10.14 8 — — — — — — WYM48 69968.1 80.0 L 29 987.5 0.02 17 10.3 0.14 6LAB259 69399.7 73.8 0.02 19 979.2 0.04 16 10.0 0.21 3 LAB259 69401.673.8 0.02 19 987.5 0.03 17 10.3 0.17 6 CONT. — 62.0 — — 845.5 — — 9.8 —— WYM48 69968.4 86.3 L 28 883.9 0.02 25 10.1 0.19 5 WYM32 70415.3 80.40.02 19 829.2 0.06 17 10.0 0.24 3 WYM18 70937.6 — — — 779.2 0.27 10 — —— WYM48 69973.4 — — — — — — 10.0 0.22 4 CONT. — 67.5 — — 706.5 — — 9.6 —— WYM18 70937.3 77.5 0.04 17 858.3 0.16 6 10.5 0.11 5 WYM32 70416.1187.4 0.02 32 1097.0 0.01 35 11.0 0.04 9 WYM30 69670.3 73.4 0.13 11 — — —— — — WYM83 70952.1 70.9 0.21 7 — — — — — — WYM61 69978.2 79.1 0.06 20947.6 0.14 17 — — — WYM18 70938.5 80.8 0.08 22 945.2 0.10 16 10.5 0.10 5WYM61 69974.1 70.0 0.19 6 — — — — — — WYM87 70962.4 72.7 0.16 10 — — — —— — CONT. — 66.1 — — 813.0 — — 10.1 — — WYM105 70931.1 74.6 0.27 9 945.80.24 12 — — — WYM48 69970.4 78.1 0.10 15 981.0 0.13 16 — — — LAB25969402.1 73.4 0.20 8 948.4 0.11 12 — — — LYM91 69395.3 89.8 L 32 1130.90.01 33 10.3 0.11 4 WYM32 70416.4 — — — 887.5 0.29 5 — — — WYM87 70962.583.0 0.02 22 1107.1 0.01 31 10.7 0.06 8 WYM61 69979.4 82.5 0.08 211070.8 0.03 26 10.2 0.26 3 WYM87 70960.2 78.6 0.05 15 968.5 0.11 14 — —— CONT. — 68.2 — — 848.2 — — 9.9 — — WYM83 70956.4 64.6 0.11 10 675.00.19 6 — — — WYM86 70917.2 66.2 0.04 13 704.8 L 10 9.5 0.24 2 WYM6169977.1 — — — — — — 9.8 0.23 4 WYM30 69670.2 61.8 0.15 6 679.8 0.10 79.6 0.20 3 LAB259 69399.6 74.2 L 27 833.3 L 31 9.9 0.10 6 WYM61 69977.467.5 0.05 15 747.6 L 17 — — — WYM30 69670.1 72.1 L 23 812.5 L 27 10.20.02 9 LYM91 69394.2 60.9 0.19 4 683.3 0.07 7 — — — CONT. — 58.6 — —637.9 — — 9.3 — — WYM105 70928.2 69.0 0.01 17 769.0 0.01 22 9.9 0.09 6WYM18 70936.4 — — — — — — 9.7 0.21 4 WYM86 70917.1 — — — — — — 9.7 0.224 WYM86 70918.7 64.6 0.07 9 929.2 0.13 48 9.8 0.16 5 LAB259 69403.2 62.60.27 6 715.5 0.09 14 10.1 0.15 9 WYM61 69977.3 — — — 670.2 0.26 7 — — —WYM18 70937.11 71.7 L 21 812.5 L 29 9.8 0.17 5 CONT. — 59.1 — — 628.1 —— 9.3 — — WYM48 69973.1 63.4 0.24 10 800.0 0.16 10 10.0 0.04 10 WYM8770962.2 — — — 768.1 0.24 5 9.3 0.07 3 WYM86 70920.4 — — — — — — 10.00.07 11 LYM91 69392.2 — — — — — — 9.6 0.04 6 WYM48 69973.5 60.9 0.26 6812.5 0.08 12 9.8 0.02 8 WYM32 70416.6 — — — — — — 10.2 L 12 LYM9169392.4 64.2 0.14 12 820.8 0.09 13 9.8 0.02 8 LYM91 69393.1 — — — — — —9.8 L 8 CONT. — 5.6 — — 728.1 — — 9.1 — — WYM62 71467.5 — — — — — — 11.50.04 9 LYM490_H1 71155.4 200.0 0.23 5 2829.2 0.24 4 11.3 0.08 7 WYM4671151.5 — — — 2825.0 0.14 4 — — — CONT. — 191.0 — — 2709.4 — — 10.6 — —WYM28 71456.2 208.4 0.09 8 — — — — — — WYM46 71154.6 229.2 0.03 18 — — —— — — LYM490__H1 71158.3 — — — — — — 10.6 0.03 7 WYM96 71173.2 — — — — —— 10.1 0.13 2 WYM46 71150.5 206.3 0.25 6 — — — — — — WYM71 72157.7 218.90.20 13 — — — — — — CONT. — 193.8 — — 2625.0 — — 9.9 — — WYM35 71163.1172.9 0.27 2 — — — — — — WYM90 71891.2 181.3 0.12 7 2550.0 0.07 6 10.4 L5 CONT. — 169.4 — — 2406.3 — — 9.9 — — LYM490_H1 71157.1 188.3 0.11 6 —— — — — — WYM46 71151.1 189.2 0.17 6 2366.7 0.17 4 — — — WYM21 71762.4186.3 0.10 5 — — — — — — WYM71 72158.1 188.8 0.08 6 2345.8 0.27 3 9.80.24 3 CONT. — 178.0 — — 2270.8 — — 9.5 — — WYM112 69928.3 171.7 0.01 142354.2 0.02 11 9.9 0.12 5 LYM490_H1 71155.2 169.2 L 13 2416.7 0.01 1410.3 0.01 10 WYM34 71768.2 158.8 0.07 6 2254.2 0.08 7 9.9 0.06 6 WYM9071891.6 — — — — — — 9.7 0.23 3 WYM28 71457.6 — — — — — — 9.8 0.13 4WYM34 71769.1 170.4 L 13 2520.8 L 19 10.0 0.07 6 WYM28 71457.2 158.40.07 5 2187.5 0.23 4 9.6 0.21 3 WYM71 72162.1 154.6 0.17 3 2254.2 0.08 79.6 0.26 3 CONT. — 150.2 — — 2113.0 — — 9.4 — — WYM35 71166.2 183.8 0.177 2675.0 0.11 5 — — — WYM71 72162.3 189.6 0.08 10 2620.8 0.23 3 — — —WYM71 72157.3 181.7 0.29 5 — — — 10.7 0.03 6 CONT. — 172.5 — — 2548.8 —— 10.1 — — WYM34 71767.6 — — — — — — 9.9 0.30 1 WYM96 71176.3 — — — — —— 10.2 0.19 4 WYM71 72157.10 199.2 0.11 5 2779.2 0.10 4 9.9 0.23 2 CONT.— 190.0 — — 2662.5 — — 9.8 — — WYM46 71150.6 187.1 0.06 7 2612.5 0.15 510.0 0.29 2 WYM21 71763.3 — — — 2616.7 0.17 5 10.3 0.09 4 CONT. — 174.5— — 2492.5 — — 9.8 — — WYM112 69931.2 — — — — — — 10.2 0.07 3 WYM3571166.1 189.8 0.23 2 2578.6 0.20 2 — — — WYM62 71467.7 — — — — — — 10.10.24 2 WYM96 71178.1 190.0 0.23 2 2608.3 0.11 3 — — — WYM21 71761.1 — —— 2608.3 0.21 3 10.1 0.18 2 WYM35 71161.1 — — — 2625.6 0.08 4 — — —CONT. — 186.0 — — 2521.9 — — 9.9 — — WYM21 71762.6 183.4 L 10 2650.0 L11 — — — WYM46 71149.5 170.4 0.22 2 — — — — — — CONT. — 167.2 — — 2397.9— — 10.2 — — WYM96 71178.3 — — — 2504.2 0.12 7 10.6 0.02 8 WYM90 71889.1185.0 0.13 8 2683.3 0.02 14 10.5 0.03 7 WYM112 69926.4 — — — — — — 10.30.15 4 CONT. — 171.9 — — 2346.9 — — 9.8 — — WYM35 71162.9 — — — — — —10.0 0.12 3 WYM90 71888.2 189.2 0.02 12 2587.5 0.04 9 — — — WYM11269929.1 — — — — — — 10.0 0.12 3 CONT. — 169.1 — — 2378.1 — — 9.8 — —LYM490_H1 71156.2 — — — — — — 9.7 0.29 2 WYM96 71174.1 — — — — — — 10.00.06 6 WYM96 71176.2 — — — — — — 9.9 0.04 5 WYM62 71466.2 — — — — — —9.8 0.15 3 WYM90 71888.1 196.5 0.08 6 2648.8 0.06 6 10.2 0.03 8 WYM7172160.5 — — — — — — 9.7 0.16 2 CONT. — 185.3 — — 2495.1 — — 9.5 — —WYM34 71766.6 — — — — — — 10.0 0.17 3 WYM71 72162.2 — — — — — — 10.20.08 5 WYM96 71173.3 — — — — — — 10.2 0.06 5 WYM28 71456.1 — — — — — —9.9 0.29 2 WYM62 71466.4 222.5 0.25 5 — — — 10.0 0.18 4 CONT. — 211.3 —— 2660.0 — — 9.7 — — WYM79 69537.4 198.4 0.05 18 2808.3 0.08 14 9.7 0.068 WYM70 70034.6 192.1 0.03 14 2612.5 0.27 6 9.9 0.05 10 WYM79 69537.3190.2 0.03 13 2542.9 0.19 3 9.5 0.20 6 WYM24 69663.3 211.3 L 26 2979.2 L21 — — — LYM320 69406.3 188.5 L 12 2567.9 0.24 4 — — — WYM79 69537.2175.9 0.22 5 — — — — — — WYM93 69690.2 182.1 0.08 8 — — — — — — WYM9469628.3 183.5 0.07 9 2535.1 0.25 3 9.3 0.19 3 CONT. — 167.9 — — 2466.7 —— 9.0 — — WYM24 69667.7 202.1 0.24 6 — — — 9.3 0.14 5 WYM79 69536.2 — —— — — — 9.3 0.01 5 WYM15 69495.5 — — — — — — 9.3 0.11 4 WYM70 70034.2204.2 0.19 7 — — — 9.4 L 6 WYM31 69730.7 — — — — — — 9.1 0.20 2 CONT. —190.5 — — 2662.5 — — 8.9 — — WYM94 69629.2 — — — — — — 9.3 0.17 3 WYM1569495.4 — — — 2708.3 0.28 3 9.1 0.28 1 CONT. — 181.3 — — 2634.4 — — 9.0— — LYM320 69405.2 — — — — — — 9.3 0.20 4 WYM70 70038.4 — — — — — — 9.40.21 5 CONT. — 221.0 — — 2490.6 — — 9.0 — — WYM31 69731.1 201.2 0.05 122769.0 0.06 16 — — — WYM94 69631.2 197.9 0.02 10 2666.7 L 12 — — — WYM3169730.4 187.7 0.09 4 2523.8 0.10 6 — — — LYM320 69409.1 199.6 L 112704.2 0.01 13 9.3 0.21 3 WYM65 69521.1 200.9 0.02 12 2891.7 0.03 21 — —— WYM65 69520.1 — — — 2420.8 0.30 2 — — — WYM70 70038.1 195.0 L 8 2695.80.02 13 — — — WYM31 69729.2 186.3 0.12 4 2562.5 0.02 7 — — — CONT. —179.9 — — 2383.9 — — 9.1 — — WYM55 69509.6 202.8 0.24 8 2512.5 0.17 10 —— — WYM15 69497.2 — — — — — — 9.3 0.17 6 WYM93 69686.1 203.8 0.22 8 — —— 9.3 0.05 6 WYM15 69495.2 — — — — — — 9.3 0.07 6 WYM70 70039.2 — — — —— — 9.1 0.14 3 WYM79 69541.2 — — — — — — 9.7 L 9 WYM55 69509.5 — — — — —— 9.0 0.14 2 CONT. — 188.4 — — 2287.5 — — 8.8 — — WYM22 69501.2 — — —2762.5 0.19 25 — — — WYM93 69686.2 190.8 0.11 4 2566.7 L 16 — — — WYM7070039.7 202.5 0.07 10 2641.7 L 19 9.4 0.08 6 LYM320 69406.1 — — — — — —9.9 0.01 12 WYM65 69519.5 196.3 0.11 7 2429.2 0.03 9 9.4 0.11 6 WYM6569520.4 203.8 L 11 2495.8 0.09 12 9.5 0.04 8 CONT. — 183.5 — — 2218.8 —— 8.8 — — WYM24 69664.1 177.5 0.29 3 2641.7 0.27 3 9.3 0.21 5 WYM2269501.5 184.2 0.05 7 2912.5 L 14 — — — WYM79 69540.2 187.1 0.07 9 2858.30.03 11 9.2 0.10 4 WYM22 69504.6 — — — — — — 9.0 0.26 3 WYM93 69686.4 —— — — — — 9.4 0.04 7 CONT. — 171.6 — — 2565.6 — — 8.8 — — WYM15 69498.1— — — 2341.7 0.17 6 — — — WYM93 69688.2 — — — — — — 9.1 0.25 3 WYM9469626.6 — — — — — — 9.1 0.28 2 CONT. — 203.5 — — 2218.8 — — 8.9 — —WYM31 69729.3 — — — — — — 9.1 0.17 3 WYM94 69628.1 — — — — — — 9.4 0.086 WYM65 69519.3 188.8 0.17 4 2290.5 0.10 6 9.3 0.14 5 WYM94 69629.3197.5 0.07 9 2316.7 0.03 7 9.0 0.29 1 CONT. — 180.8 — — 2165.0 — — 8.9 —— WYM93 69687.3 — — — 2133.3 0.19 7 — — — WYM65 69519.1 158.6 0.20 62132.7 0.19 7 — — — WYM65 69523.2 165.9 0.11 11 2166.7 0.20 9 — — —WYM22 69500.5 159.2 0.24 7 2166.7 0.18 9 — — — WYM79 69538.3 166.3 0.1212 2291.7 0.05 15 9.3 0.20 4 WYM22 69504.5 159.2 0.20 7 2186.3 0.16 10 —— — WYM79 69538.1 164.6 0.11 11 2333.3 0.04 17 9.2 0.29 3 CONT. — 149.0— — 1996.0 — — 8.9 — — WYM24 69662.2 214.2 0.05 12 2587.5 0.11 8 9.30.26 2 WYM94 69630.1 — — — — — — 9.3 0.29 2 WYM24 69662.1 202.1 0.19 62516.7 0.22 5 9.3 0.23 2 WYM93 69688.1 213.8 0.05 12 — — — 9.6 0.04 5WYM22 69500.8 210.0 0.09 10 2539.9 0.18 6 — — — WYM70 70034.7 200.7 0.225 — — — — — — CONT. — 191.4 — — 2399.7 — — 9.1 — — WYM55 69507.2 — — — —— — 9.7 0.08 3 WYM79 69536.1 206.7 0.02 10 2500.0 L 13 9.6 0.16 3 WYM5569510.2 — — — 2408.3 0.09 8 — — — WYM70 70039.6 200.4 0.10 7 2512.5 0.0213 9.8 0.06 5 WYM22 69504.3 204.0 0.25 9 2637.9 0.08 19 — — — WYM2269504.2 207.9 0.02 11 2554.2 L 15 — — — LYM320 69405.3 — — — 2325.0 0.185 9.9 0.05 6 WYM93 69690.3 — — — 2412.5 0.10 9 — — — CONT. — 187.5 — —2221.9 — — 9.3 — — WYM31 69730.5 — — — — — — 9.1 0.19 1 WYM15 69494.2 —— — 2287.5 0.27 6 9.2 0.24 2 CONT. — 157.5 — — 2162.5 — — 9.0 — —LYM208_H4 69488.5 135.9 0.11 8 — — — — — — WYM16 69883.9 144.6 0.03 151683.3 0.05 12 10.2 0.22 1 WYM16 69883.7 132.1 0.11 5 — — — — — — WYM2569725.4 133.3 0.23 6 — — — — — — WYM16 69883.4 136.7 0.06 9 1570.8 0.234 — — — WYM25 69726.1 — — — 1554.2 0.27 3 10.7 0.08 6 WYM81 69542.6130.0 0.25 4 — — — — — — LYM208_H4 69489.10 137.2 0.07 9 1615.8 0.21 7 —— — LYM208_H4 69490.1 — — — 1607.1 0.22 7 — — — LYM208_H4 69490.2 — — —— — — 10.5 0.07 4 WYM81 69542.3 — — — — — — 10.3 0.23 2 WYM25 69724.1149.2 L 19 1854.2 0.07 23 10.3 0.20 2 WYM25 69726.5 145.4 0.09 16 1779.20.03 18 10.6 0.13 5 LYM208_H4 69489.5 132.5 0.19 6 — — — — — — LYM208_H469488.1 142.9 0.19 14 1600.0 0.11 6 — — — CONT. — 125.6 — — 1506.0 — —10.1 — — WYM64 72486.1 259.2 0.08 9 4008.3 0.18 7 — — — WYM38 71688.4262.9 0.07 10 — — — — — — WYM38 71688.3 250.3 0.22 5 — — — — — — WYM1271897.1 261.3 0.09 9 — — — — — — WYM85 71526.6 278.4 0.02 17 4145.8 0.1011 — — — WYM103 71449.1 263.4 0.08 10 — — — — — — WYM29 71879.3 277.90.03 16 4016.7 0.17 7 — — — WYM103 71450.3 263.9 0.06 11 — — — — — —CONT. — 238.8 — — 3743.8 — — 10.8 — — WYM103 71451.1 275.9 0.13 3 4033.30.13 5 10.5 0.29 4 WYM113 72759.6 — — — 3991.7 0.17 4 11.0 0.14 8 WYM11372761.2 277.0 0.23 3 — — — 11.4 0.07 12 CONT. — 268.4 — — 3854.2 — —10.2 — — WYM3 72479.5 — — — 4219.6 0.26 9 — — — WYM64 72486.2 360.0 0.118 4570.8 0.12 18 — — — WYM20 72487.2 — — — 4133.3 0.23 7 — — — WYM269654.2 345.0 0.25 4 4279.2 0.02 11 — — — WYM38 71693.5 356.7 0.17 74080.4 0.09 6 11.1 0.11 6 WYM38 71689.4 353.0 0.25 6 4162.5 0.04 8 — — —WYM3 72475.3 — — — 4472.0 0.02 16 — — — WYM3 72476.1 364.6 0.07 104495.8 L 16 — — — CONT. — 331.9 — — 3865.6 — — 10.5 — — LAB278_H071521.3 — — — — — — 11.0 0.25 4 WYM113 72762.7 — — — — — — 10.8 0.29 3WYM85 71527.3 271.3 0.04 6 4133.3 0.15 5 — — — WYM29 71877.2 274.2 0.028 — — — 11.4 0.04 8 WYM20 72492.1 280.0 0.06 10 4000.0 0.29 2 11.6 0.0310 WYM38 71690.2 276.7 0.02 9 4083.3 0.16 4 10.9 0.18 3 WYM64 72485.8282.1 0.06 11 4354.2 0.05 11 10.9 0.13 4 CONT. — 254.7 — — 3918.8 — —10.5 — — WYM3 72477.1 — — — 3862.5 0.21 4 — — — WYM103 71451.2 276.30.25 4 — — — — — — WYM3 72479.7 289.5 0.05 9 4072.0 0.05 10 — — — CONT.— 266.3 — — 3706.3 — — 11.2 — — WYM20 72491.5 — — — 4475.0 0.25 4 — — —WYM113 72762.1 — — — 4687.5 0.11 9 11.1 0.06 8 WYM12 71892.4 — — —4626.2 0.15 7 10.6 0.23 4 WYM85 71529.3 — — — 4791.7 0.02 11 10.7 0.18 4WYM12 71893.4 — — — 4783.3 0.05 11 10.6 0.22 4 WYM85 71528.4 — — —4695.8 0.16 9 10.8 0.15 6 CONT. — 362.9 — — 4312.5 — — 10.2 — —LAB278_H0 71522.4 294.2 0.14 9 4183.3 0.09 8 — — — WYM12 71893.9 301.50.01 12 4355.4 0.02 13 — — — WYM38 71690.3 310.0 L 15 4475.0 L 16 11.00.10 7 WYM20 72491.6 298.8 0.01 11 4337.5 L 12 — — — WYM64 72481.7 325.70.02 21 4782.7 0.01 24 — — — WYM12 71895.1 282.1 0.07 5 4087.5 0.10 6 —— — WYM113 72761.4 287.1 0.17 7 4112.5 0.14 6 — — — CONT. — 269.5 — —3864.3 — — 10.3 — — WYM12 71892.3 306.7 0.18 3 — — — — — — WYM38 71688.1306.3 0.02 3 — — — — — — CONT. — 298.8 — — 4275.0 — — 10.7 — — WYM2971876.3 — — — — — — 10.2 0.28 2 WYM3 72479.2 305.9 0.04 18 3941.7 0.24 510.9 0.07 10 WYM3 72475.4 274.6 0.02 6 4100.0 0.07 9 10.1 0.23 2LAB278_H0 71521.5 291.7 0.07 13 4250.0 L 13 — — — LAB278_H0 71522.7268.4 0.22 4 3941.7 0.20 5 — — — WYN438 71689.2 281.7 L 9 4054.2 0.05 810.9 L 9 CONT. — 259.1 — — 3765.6 — — 10.0 — — WYM3 72478.3 304.2 L 114537.5 L 15 10.7 0.26 3 WYM38 71689.6 277.9 0.24 1 4029.2. 0.28 L — — —WYM85 71527.5 296.1 0.12 8 4216.1 0.07 7 10.5 0.20 1 LAB278_H0 71521.2282.1 0.11 3 4116.7 0.11 4 — — — CONT. — 274.4 — — 3946.9 — — 10.4 — —LAB278_H0 71522.3 — — — 4283.3 0.06 8 — — — CONT. — 327.0 — — 3970.0 — —10.7 — — WYM29 71877.4 — — — — — — 10.9 L 3 WYM64 72485.4 — — — — — —11.1 0.09 5 WYM64 72486.3 — — — — — — 10.7 0.26 1 WYN438 71688.2 372.50.05 11 4445.8 0.22 2 — — — CONT. — 334.4 — — 4362.5 — — 10.6 — — WYM11372762.5 573.8 0.22 78 — — — 11.1 0.02 16 WYM20 72489.5 — — — — — — 10.20.13 6 WYM2 69650.2 — — — — — — 10.1 0.16 5 WYM29 71876.5 — — — — — —10.8 0.03 13 WYM12 71896.5 — — — — — — 10.9 0.06 13 WYM64 72485.2 — — —— — — 10.3 0.14 6 WYM85 71526.3 — — — 4262.5 0.28 4 10.7 0.06 11 WYM11372762.4 — — — — — — 10.5 0.17 9 CONT. — 322.1 — — 4107.2 — — 9.6 — —WYM103 71452.3 — — — 3991.7 0.19 4 11.3 L 12 WYM64 72485.10 — — — — — —10.2 0.23 1 WYM3 72479.9 294.2 0.22 11 — — — 11.2 L 11 WYM113 72762.3 —— — — — — 11.0 0.02 9 WYM85 71526.5 — — — 3970.8 0.28 3 10.8 0.09 8WYM103 71450.5 — — — 3962.5 0.26 3 11.1 L 11 CONT. — 266.0 — — 3845.1 —— 10.0 — — WYM42 69677.3 150.1 0.29 14 — — — — — — LYM350 69417.1 156.30.25 19 1354.2 0.23 9 11.0 L 6 WYM42 69679.5 155.9 0.22 19 1420.8 0.2614 10.7 0.16 3 LYM350 69418.3 140.9 0.24 7 — — — — — — LYM350 69418.6144.2 0.24 10 — — — — — — LYM350 69418.5 — — — — — — 10.7 0.18 3 WYM4269677.1 141.3 0.18 7 — — — — — — CONT. — 131.5 — — 1244.6 — — 10.4 — —WYM72 70043.1 135.8 0.21 6 1533.3 0.27 6 10.1 0.09 4 WYM91 70012.10154.2 0.17 20 1733.3 0.09 20 10.2 0.21 5 WYM72 70043.5 162.9 L 27 1718.5L 19 10.0 0.12 3 WYM43 69949.7 150.4 L 17 1679.2 0.11 16 10.0 0.12 3WYM91 70011.7 136.5 0.29 6 1513.9 0.25 5 — — — WYM72 70045.9 — — — — — —10.0 0.18 4 WYM23 69658.2 145.7 0.03 13 1635.1 0.05 13 10.5 L 8 WYM6770023.2 171.7 0.03 33 1922.6 L 33 10.8 L 12 WYM43 69947.4 139.2 0.22 81587.5 0.24 10 10.5 0.03 8 WYM91 70012.4 142.1 0.28 10 — — — — — — WYM4369949.3 141.7 0.09 10 1695.8 0.12 17 10.1 0.02 4 WYM91 70012.7 159.60.07 24 1845.8 0.07 28 10.6 L 9 WYM72 70044.3 139.6 0.22 8 1570.8 0.22 910.2 0.10 5 WYM23 69656.1 — — — — — — 9.8 0.27 2 WYM43 69947.5 138.80.29 8 — — — 10.2 0.08 5 WYM72 70043.7 145.8 0.13 13 1716.7 0.09 19 10.50.03 8 WYM67 70022.3 — — — — — — 10.0 0.14 3 WYM23 69658.4 145.4 0.30 131616.7 0.30 12 10.0 0.11 4 WYM72 70045.2 — — — 1546.4 0.2.0 7 — — —WYM72 70044.1 — — — 1519.4 0.25 5 10.1 L 4 WYM72 70045.3 — — — 1511.80.17 5 10.0 0.17 3 WYM43 69944.4 138.8 0.25 8 1579.2 0.22 9 10.4 L 8WYM67 70022.10 — — — 1586.3 0.28 10 — — — WYM43 69949.10 140.9 0.06 91658.3 0.04 15 10.4 L 7 WYM67 70023.1 157.0 L 22 1776.8 0.04 23 10.30.19 6 WYM23 69657.4 151.3 0.04 18 1716.7 0.05 19 9.9 0.09 2 WYM7270043.2 148.3 0.19 15 1675.0 0.16 16 10.6 0.13 9 WYM43 69949.6 132.50.29 3 — — — 10.3 0.12 7 WYM67 70022.2 — — — 1591.7 0.27 10 10.0 0.18 3WYM67 70023.3 — — — 1595.8 0.15 10 10.0 0.08 4 WYM23 69660.3 — — —1591.7 0.20 10 — — — WYM23 69661.7 — — — — — — 10.2 0.09 5 WYM23 69661.7142.1 0.10 10 1629.2 0.12 13 10.3 0.01 6 WYM43 69949.11 169.4 0.17 321601.2 0.23 11 — — — CONT. — 128.7 — — 1446.0 — — 9.7 — — WYM74 69531.2— — — 1329.2 0.26 7 — — — WYM74 69531.3 128.3 0.21 7 1307.7 0.25 5 — — —WYM74 69535.2 123.8 0.26 3 — — — — — — WYM69 69528.5 124.2 0.30 3 — — —— — — WYM69 69529.2 127.5 0.11 6 — — — — — — CONT. — 120.2 — — 1246.7 —— 10.6 — — Table 60. “CONT.” - Control; “Ave.” - Average; “% Incr” = %increment; “p-val.” - p-value, L - p < 0.01.

TABLE 61 Genes showing improved plant performance at normal growthconditions under regulation of At6669 promoter Rosette Area [cm²]Rosette Diameter [cm] % % Gene Name Event # Ave. P-Val. Incr. Ave.P-Val. Incr. LAB259 69401.8 8.3 0.02 28 5.2 L 18 WYM18 70938.3 9.0 L 395.3 L 20 WYM86 70919.5 7.4 0.24 14 4.7 0.26 6 WYM30 69672.2 8.4 0.05 295.1 0.05 14 WYM83 70956.7 8.1 0.03 26 5.1 0.04 14 WYM83 70953.1 9.2 L 425.4 L 21 WYM105 70931.3 7.7 0.06 19 4.9 0.07 10 CONT. — 6.5 — — 4.4 — —WYM48 69972.5 7.8 L 32 4.8 0.02 14 WYM105 70928.1 6.3 0.23 6 4.4 0.26 4WYM86 70917.3 8.5 L 43 5.0 0.01 19 WYM32 70412.2 6.5 0.10 10 4.4 0.22 5LAB259 69400.1 7.4 0.01 24 4.9 0.02 15 WYM30 69668.2 6.4 0.17 8 4.5 0.156 LYM91 69394.5 6.4 0.16 8 4.5 0.11 7 CONT. — 5.9 — — 4.2 — — WYM6169974.2 7.8 0.21 8 4.8 0.24 4 WYM83 70951.3 7.7 0.28 7 — — — WYM8670918.6 9.0 0.03 26 5.2 0.03 14 WYM105 70930.2 8.6 0.06 20 5.0 0.09 9WYM32 70415.2 8.2 0.11 14 — — — WYM18 70938.6 8.8 0.04 23 5.1 0.07 10WYM83 70951.4 10.1 L 41 5.6 L 20 CONT. — 7.2 — — 4.6 — — WYM86 70919.27.6 0.11 10 4.8 0.05 8 WYM87 70960.8 7.6 0.11 11 4.9 0.08 10 WYM3270414.3 8.3 0.01 20 5.0 L 13 WYM32 70413.2 8.0 0.03 17 4.9 L 10 WYM8370956.5 7.6 0.15 11 4.8 0.12 8 WYM30 69672.4 8.2 0.01 20 5.0 L 13 LYM9169395.2 7.8 0.04 14 4.8 0.03 8 CONT. — 6.9 — — 4.4 — — WYM30 69673.2 — —— 5.3 0.30 3 WYM61 69977.2 — — — 5.3 0.19 3 WYM18 70938.7 11.3 0.02 215.7 0.04 11 WYM87 70960.3 9.8 0.23 5 5.4 0.11 4 WYM32 70416.3 — — — 5.30.13 4 CONT. — 9.3 — — 5.1 — — WYM105 70932.10 6.5 0.28 5 4.5 0.19 3WYM87 70961.6 — — — 4.4 0.25 2 LYM91 69395.1 — — — 4.5 0.21 3 WYM8770961.7 — — — 4.5 0.18 3 WYM105 70930.1 6.6 0.26 6 — — — WYM30 69672.1 —— — 4.5 0.23 3 LAB259 69401.1 7.1 0.06 14 4.9 L 13 CONT. — 6.2 — — 4.3 —— WYM32 70417.1 7.5 0.01 20 4.9 0.02 13 WYM86 70919.1 6.8 0.10 8 4.70.06 8 WYM83 70953.2 7.2 0.18 15 4.7 0.20 8 WYM83 70956.1 7.1 0.03 144.7 0.06 8 WYM86 70920.1 8.0 L 28 5.0 L 16 CONT. — 6.2 — — 4.3 — — WYM4869972.3 7.9 0.19 6 5.0 0.16 4 LYM91 69392.6 8.0 0.28 9 5.0 0.26 4 WYM4869968.1 8.2 0.09 12 5.2 0.04 8 LAB259 69399.7 8.3 0.06 13 5.1 0.11 6LAB259 69401.6 8.4 0.06 14 5.2 0.04 8 CONT. — 7.4 — — 4.8 — — WYM4869968.4 8.2 0.06 15 4.9 0.12 5 WYM32 70415.3 8.1 0.11 14 5.0 0.18 6WYM87 70961.8 7.8 0.02 9 4.9 0.07 4 WYM18 70938.1 7.4 0.11 4 4.8 0.14 2WYM48 69973.4 7.7 0.05 8 4.9 0.03 4 CONT. — 7.1 — — 4.7 — — WYM1870937.3 8.8 0.10 11 5.2 0.08 6 WYM32 70416.11 10.3 L 31 5.7 L 16 WYM3069670.3 8.5 0.18 7 5.2 0.18 5 WYM61 69978.2 9.3 0.03 17 5.5 0.04 12WYM18 70938.5 9.4 0.10 18 5.4 0.05 10 CONT. — 7.9 — — 4.9 — — WYM10570931.1 9.0 0.17 20 5.0 0.16 12 WYM48 69970.4 8.5 0.19 14 4.9 0.18 9LAB259 69402.1 8.0 0.18 7 4.7 0.13 4 LYM91 69395.3 9.9 0.01 33 5.2 0.0315 WYM32 70416.4 8.9 0.05 20 5.0 0.03 11 WYM87 70962.5 10.5 0.01 40 5.40.01 20 WYM61 69979.4 9.7 0.04 30 5.3 0.03 18 WYM87 70960.2 8.8 0.19 194.9 0.18 9 CONT. — 7.5 — — 4.5 — — WYM83 70956.4 7.3 0.03 13 4.6 0.03 9WYM86 70917.2 7.0 0.11 10 4.6 0.05 10 WYM61 69977.1 7.1 0.13 11 4.6 0.0211 WYM30 69670.2 7.4 L 16 4.6 0.03 9 LAB259 69399.6 8.8 L 38 5.0 L 19WYM61 69977.4 7.8 L 21 4.7 0.02 12 WYM30 69670.1 8.6 L 33 4.8 L 16 LYM9169394.2 7.0 0.12 9 4.4 0.07 6 CONT. — 6.4 — — 4.2 — — WYM105 70928.2 8.10.11 14 5.0 0.12 9 WYM86 70918.7 8.2 0.05 15 5.1 0.04 11 LAB259 69403.27.5 0.21 6 4.7 0.26 3 WYM18 70937.11 8.7 0.02 22 5.0 0.06 9 CONT. — 7.1— — 4.6 — — WYM48 69973.1 8.1 0.06 16 5.1 0.04 11 WYM86 70920.4 7.3 0.284 4.8 0.14 4 WYM48 69973.5 8.0 0.10 14 5.0 0.06 8 WYM32 70416.6 7.7 0.1010 4.8 0.13 4 LYM91 69392.4 8.0 0.04 15 5.1 0.02 10 CONT. — 7.0 — — 4.6— — WYM62 71467.5 10.6 0.07 15 5.7 0.10 7 LYM490_H1 71155.4 11.1 0.04 215.8 0.05 10 CONT. — 9.2 — — 5.3 — — LYM490_H1 71158.3 8.5 0.29 4 — — —CONT. — 8.2 — — 5.0 — — WYM35 71163.1 8.8 0.04 15 5.3 0.04 8 WYM9071891.2 8.5 0.08 11 5.2 0.09 7 CONT. — 7.6 — — 4.9 — — WYM46 71151.1 — —— 4.7 0.27 3 WYM71 72158.1 — — — 4.6 0.15 2 CONT. — 6.8 — — 4.5 — —WYM112 69928.3 9.3 0.03 28 5.3 0.01 15 LYM490_H1 71155.2 7.8 0.25 7 4.80.18 4 WYM34 71768.2 8.0 0.17 11 5.0 0.09 7 WYM34 71769.1 9.1 0.03 255.2 0.02 12 WYM28 71457.2 8.1 0.16 12 5.0 0.08 7 WYM71 72162.1 7.9 0.219 5.0 0.05 8 CONT. — 7.3 — — 4.6 — — WYM35 71166.2 8.9 0.29 5 — — —CONT. — 8.5 — — 5.2 — — WYM112 69928.1 — — — 5.3 0.26 4 WYM21 71763.310.0 0.02 23 5.5 0.04 9 CONT. — 8.1 — — 5.1 — — WYM62 71467.7 8.8 0.04 85.3 0.02 5 WYM21 71761.1 8.8 0.07 7 5.3 0.11 4 WYM35 71161.1 — — — 5.20.12 2 CONT. — 8.2 — — 5.1 — — WYM21 71762.6 8.6 0.01 10 5.4 L 8 WYM4671150.8 8.2 0.29 4 5.1 0.21 2 CONT. — 7.9 — — 5.0 — — WYM90 71889.1 9.00.06 11 5.4 0.09 5 WYM112 69926.4 8.4 0.28 4 5.3 0.21 3 CONT. — 8.1 — —5.1 — — WYM35 71162.9 9.1 0.06 17 5.3 0.07 8 WYM90 71888.2 8.2 0.27 5 —— — CONT. — 7.8 — — 4.9 — — LYM490_H1 71156.2 7.1 0.05 6 4.7 0.10 4WYM96 71174.1 7.5 0.06 11 4.7 0.12 4 WYM34 71766.1 6.8 0.29 1 — — —WYM90 71888.1 8.0 0.02 20 4.9 0.01 8 WYM71 72160.5 7.1 0.15 6 — — —CONT. — 6.7 — — 4.5 — — WYM7I 72162.2 8.7 0.17 5 5.3 0.07 4 CONT. — 8.2— — 5.1 — — WYM79 69537.4 6.9 0.02 47 4.5 0.01 21 WYM70 70034.6 6.1 0.0330 4.2 0.02 13 WYM79 69537.3 6.0 L 29 4.2 L 13 WYM24 69663.3 5.7 L 224.3 L 14 LYM320 69406.3 5.5 0.06 17 4.0 0.09 7 WYM79 69537.2 5.3 0.11 144.1 0.02 10 WYM93 69690.2 5.8 L 24 4.2 L 11 WYM94 69628.3 5.9 0.05 264.3 0.05 14 CONT. — 4.7 — — 3.7 — — WYM94 69631.1 5.1 0.21 5 3.9 0.08 3WYM24 69667.7 6.5 0.03 34 4.4 0.04 17 WYM79 69536.2 5.4 0.06 13 4.1 0.059 WYM31 69730.9 5.2 0.22 7 4.0 0.07 5 WYM15 69495.5 5.6 0.07 17 4.1 0.098 WYM70 70034.2 6.1 L 27 4.3 L 12 WYM31 69730.7 5.6 0.02 16 4.2 0.02 10WYM15 69497.4 5.2 0.21 7 4.0 0.14 5 CONT. — 4.8 — — 3.8 — — WYM9469629.2 5.4 0.06 11 4.1 0.10 6 WYM15 69495.4 5.3 0.11 9 4.1 0.13 5 CONT.— 4.9 — — 3.9 — — WYM31 69731.1 5.3 0.17 9 4.0 0.24 4 WYM94 69631.2 5.90.11 22 4.3 0.07 13 WYM31 69730.4 5.3 0.13 9 4.1 0.05 7 LYM320 69409.15.7 0.03 18 4.1 0.04 8 WYM65 69521.1 5.1 0.21 6 3.9 0.19 3 WYM65 69520.1— — — 3.9 0.26 3 WYM70 70038.1 5.3 0.12 9 4.0 0.11 4 CONT. — 4.8 — — 3.8— — WYM55 69509.6 — — — 4.0 0.28 2 WYM15 69497.2 5.7 0.20 15 4.1 0.24 6WYM15 69499.5 5.5 0.14 11 4.2 0.06 8 WYM93 69686.1 5.7 0.09 14 4.2 0.097 WYM15 69495.2 6.5 0.03 31 4.5 0.02 16 WYM70 70039.2 5.4 0.24 9 4.10.25 4 WYM79 69541.2 6.7 0.02 34 4.5 0.01 16 WYM55 69509.5 5.8 0.09 174.2 0.08 8 CONT. — 5.0 — — 3.9 — — WYM31 69729.1 5.8 0.14 11 4.2 0.17 5WYM93 69686.2 5.5 0.29 6 4.2 0.22 3 WYM70 70039.7 6.2 0.03 19 4.4 0.02 9LYM320 69406.1 6.3 0.02 21 4.2 0.07 5 WYM65 69519.5 5.7 0.14 9 4.1 0.183 WYM65 69520.4 5.8 0.12 10 4.3 0.10 6 CONT. — 5.2 — — 4.0 — — WYM2469664.1 5.5 0.19 9 4.1 0.24 4 WYM22 69504.6 5.4 0.17 8 — — — WYM9369686.4 5.3 0.10 6 4.1 0.24 2 CONT. — 5.0 — — 4.0 — — WYM24 69667.12 5.20.25 5 4.1 0.25 3 WYM94 69626.6 5.1 0.30 3 — — — CONT. — 5.0 — — 4.0 — —WYM31 69729.3 4.7 0.24 3 3.7 0.25 2 WYM94 69628.1 4.8 0.19 6 — — — WYM6569519.3 — — — 3.8 0.05 4 WYM94 69629.3 5.0 0.12 11 3.9 0.18 6 CONT. —4.5 — — 3.7 — — WYM65 69523.2 — — — 3.8 0.17 3 WYM79 69538.3 4.7 0.28 4— — — WYM79 69538.1 5.0 0.14 10 3.9 0.13 5 CONT. — 4.5 — — 3.7 — — WYM2469662.2 6.5 0.03 27 4.5 0.01 13 WYM94 69630.1 6.1 0.04 19 4.3 0.07 7WYM24 69662.1 6.1 0.07 20 4.3 0.12 8 WYM93 69688.1 6.5 L 27 4.5 L 13WYM79 69539.4 5.9 0.11 15 4.3 0.13 8 WYM22 69500.8 6.1 0.08 20 4.3 0.167 WYM70 70034.7 6.0 0.14 17 4.2 0.21 6 CONT. — 5.1 — — 4.0 — — WYM5569507.2 6.2 0.08 14 4.5 0.05 7 WYM79 69536.1 5.9 0.17 8 4.3 0.16 4 WYM7070039.6 6.7 0.02 23 4.6 0.03 10 WYM22 69504.2 6.4 0.05 17 4.6 0.04 9LYM320 69405.3 6.0 0.19 11 4.3 0.21 4 CONT. — 5.4 — — 4.2 — — LYM208_H469488.5 10.4 0.27 5 5.6 0.20 3 WYM16 69883.9 11.4 L 15 5.8 L 8 WYM2569725.4 — — — 5.6 0.25 4 WYM16 69883.4 10.8 0.20 9 5.6 0.19 5 LYM208_H469489.1 11.4 0.14 15 5.9 0.14 9 WYM25 69726.1 10.8 0.05 9 5.7 0.10 6WYM81 69542.6 10.7 0.08 8 5.6 0.11 5 WYM25 69725.7 10.5 0.29 6 5.6 0.214 WYM81 69542.3 11.2 0.22 13 5.8 0.20 7 WYM25 69724.1 12.6 0.06 27 6.10.05 13 WYM25 69726.5 12.0 0.01 21 5.9 0.02 9 LYM208_H4 69488.1 10.70.10 7 5.5 0.24 3 CONT. — 9.9 — — 5.4 — — WYM64 72486.1 7.4 0.05 9 4.60.02 8 WYM85 71526.6 7.8 L 15 4.6 0.02 8 WYM29 71879.3 — — — 4.4 0.14 3WYM103 71450.3 7.1 0.21 4 4.4 0.16 4 CONT. — 6.8 — — 4.3 — — WYM11372759.3 7.1 0.23 9 4.5 0.22 5 WYM103 71451.1 7.4 0.15 12 4.4 0.18 4WYM113 72759.6 7.0 0.26 8 4.4 0.20 4 WYM113 72761.2 7.7 0.09 18 4.5 0.106 CONT. — 6.5 — — 4.3 — — WYM3 72479.5 — — — 4.4 0.29 3 CONT. — 6.8 — —4.3 — — WYM85 71527.3 7.0 0.23 9 4.3 0.19 5 WYM20 72492.1 7.7 0.05 214.5 0.05 10 WYM38 71690.2 7.3 0.02 14 4.5 0.02 10 WYM64 72485.8 7.1 0.0811 4.4 0.08 6 CONT. — 6.4 — — 4.1 — — WYM3 72477.1 8.0 0.06 10 4.9 0.038 CONT. — 7.3 — — 4.5 — — WYM113 72762.1 6.9 0.20 6 4.3 0.18 3 WYM8571529.3 7.2 0.09 11 4.5 0.05 8 WYM12 71893.4 6.9 0.30 7 4.4 0.16 6 WYM8571528.4 7.0 0.12 8 4.4 0.07 5 CONT. — 6.5 — — 4.2 — — LAB278_H0 71522.4— — — 4.2 0.19 5 WYM12 71893.9 — — — 4.1 0.26 3 WYM38 71690.3 7.3 0.0223 4.5 L 13 WYM20 72491.6 6.3 0.25 6 4.2 0.07 6 WYM64 72481.7 6.9 0.0417 4.4 0.01 11 CONT. — 5.9 — — 4.0 — — WYM103 71452.1 6.4 0.26 2 — — —WYM12 71892.3 6.5 0.16 4 — — — CONT. — 6.3 — — 4.2 — — WYM3 72479.2 7.00.03 19 4.3 0.06 9 WYM3 72475.4 6.2 0.05 7 4.1 0.06 3 LAB278_H0 71521.5— — — 4.1 0.29 2 LAB278_H0 71522.7 6.3 0.21 7 4.2 0.16 4 WYM38 71689.26.2 0.15 7 4.2 0.11 4 CONT. — 5.8 — — 4.0 — — WYM3 72478.3 7.4 0.07 104.5 0.08 4 CONT. — 6.7 — — 4.3 — — WYM64 72481.2 — — — 4.5 0.11 4 CONT.— 6.8 — — 4.3 — — WYM64 72485.4 — — — 4.6 0.11 3 CONT. — 7.2 — — 4.4 — —WYM113 72762.5 5.9 0.26 3 4.0 0.16 2 WYM20 72489.5 6.5 0.05 13 4.2 0.067 WYM29 71876.5 6.1 0.11 7 4.2 0.08 6 WYM12 71896.5 6.5 0.07 14 4.1 0.105 WYM64 72485.2 6.5 0.04 13 4.2 L 7 WYM85 71526.3 6.9 L 20 4.3 L 10WYM113 72762.4 6.4 0.08 12 4.2 L 6 CONT. — 5.7 — — 3.9 — — WYM10371452.3 6.4 0.16 7 4.2 0.14 4 WYM3 72479.9 6.7 0.07 12 4.2 0.13 4 WYM8571526.5 6.2 0.30 5 4.1 0.21 3 WYM103 71450.5 6.2 0.22 5 4.1 0.30 2 CONT.— 5.9 — — 4.0 — — LYM350 69417.1 12.5 0.04 10 6.4 0.05 9 LYM350 69418.6— — — 6.1 0.23 5 LYM350 69421.2 12.8 0.16 12 6.2 0.15 7 CONT. — 11.4 — —5.9 — — WYM67 70022.7 9.6 0.04 8 5.2 0.11 3 WYM72 70043.1 10.1 0.06 145.4 0.07 8 WYM91 70012.10 10.7 0.01 21 5.6 0.01 12 WYM72 70043.5 9.90.18 12 — — — WYM43 69949.7 10.7 0.03 21 5.7 0.03 13 WYM91 70011.7 9.40.20 5 5.1 0.25 2 WYM72 70045.9 9.9 0.20 11 5.3 0.13 6 WYM91 70011.4 9.50.25 7 5.4 0.14 7 WYM23 69658.2 10.8 L 22 5.7 L 14 WYM67 70023.2 12.20.02 37 6.0 0.04 19 WYM43 69945.2 10.4 0.06 17 5.5 0.10 10 WYM43 69947.410.5 0.06 18 5.4 0.10 8 WYM91 70012.4 9.7 0.19 9 5.4 0.15 7 WYM4369949.3 11.2 0.04 26 5.9 0.02 17 WYM91 70012.7 12.2 L 37 5.9 L 18 WYM7270044.3 10.0 0.06 12 5.3 0.05 6 WYM23 69656.1 9.5 0.25 7 5.3 0.18 6WYM43 69947.5 10.3 0.08 16 5.5 0.06 10 WYM72 70043.7 12.0 0.04 35 5.90.05 18 WYM23 69659.1 10.2 0.21 14 5.3 0.26 5 WYM23 69658.4 10.2 0.20 155.4 0.21 8 WYM72 70045.2 9.7 L 9 5.3 0.07 5 WYM72 70044.1 9.8 0.11 105.4 0.08 8 WYM43 69944.4 10.8 L 21 5.9 L 18 WYM43 69949.10 10.9 0.03 225.6 0.04 12 WYM67 70023.1 11.0 0.06 24 5.7 0.05 13 WYM23 69657.4 10.5 L18 5.7 L 13 WY.M72 70043.2 11.5 0.06 29 5.7 0.07 13 WYM43 69949.6 10.20.05 15 5.4 0.02 8 WYM67 70023.3 10.5 0.03 18 5.5 0.10 9 WYM23 69660.311.0 0.05 24 5.6 0.05 11 WYM23 69661.4 10.3 0.08 16 5.5 0.03 10 WYM2369661.7 10.8 L 22 5.5 0.06 10 WYM43 69949.11 9.7 0.04 9 5.3 0.05 6 CONT.— 8.9 — — 5.0 — — WYM69 69529.4 — — — 5.9 0.21 2 CONT. — 11.0 — — 5.8 —— Table 61. “CONT.” - Control; “Ave.” - Average; “% Incr.” = %increment; “p-val.” - p-value, L - p < 0.01.

TABLE 62 Genes showing improved plant performance at normal growthconditions under regulation of At6669 promoter GR Of Rosette Diameter[cm/day] Gene Name Event # Ave. P-Val. % Incr. LAB259 69401.8 0.4 0.0219 WYM18 70938.3 0.4 0.01 22 WYM30 69672.2 0.4 0.10 16 WYM83 70956.7 0.40.09 16 WYM83 70953.1 0.4 0.01 24 WYM105 70931.3 0.4 0.27 9 CONT. — 0.3— — WYM48 69972.5 0.4 0.03 16 WYM86 70917.3 0.4 L 22 LAB259 69400.1 0.40.01 19 WYM30 69668.2 0.4 0.10 11 LYM91 69394.5 0.4 0.07 12 CONT. — 0.3— — WYM86 70918.6 0.4 0.10 14 WYM83 70951.4 0.4 0.03 19 CONT. — 0.4 — —WYM86 70919.2 0.4 0.14 9 WYM87 70960.8 0.4 0.14 11 WYM32 70414.3 0.40.06 11 WYM32 70413.2 0.4 0.06 12 WYM83 70956.5 0.4 0.13 11 WYM3069672.4 0.4 0.02 14 LYM91 69395.2 0.4 0.06 11 CONT. — 0.3 — — WYM1870938.7 0.5 0.21 10 CONT. — 0.4 — — WYM105 70932.10 0.4 0.29 7 LYM9169395.1 0.4 0.25 7 WYM87 70961.7 0.4 0.24 8 WYM30 69672.1 0.4 0.25 7LAB259 69401.1 0.4 L 19 CONT. — 0.3 — — WYM32 70417.1 0.4 0.01 18 WYM8670919.1 0.4 0.11 10 WYM83 70956.1 0.4 0.08 11 WYM86 70920.1 0.4 L 20CONT. — 0.3 — — WYM48 69968.1 0.4 0.13 10 LAB259 69401.6 0.4 0.11 9CONT. — 0.4 — — WYM32 70415.3 0.4 0.25 8 CONT. — 0.4 — — WYM18 70937.30.4 0.29 7 WYM32 70416.11 0.5 0.03 16 WYM61 69978.2 0.4 0.15 10 WYM1870938.5 0.4 0.21 9 CONT. — 0.4 — — WYM48 69970.4 0.4 0.24 12 LYM9169395.3 0.4 0.06 15 WYM32 70416.4 0.4 0.23 9 WYM87 70962.5 0.4 0.06 17WYM61 69979.4 0.4 0.06 16 CONT. — 0.4 — — WYM83 70956.4 0.4 0.12 10WYM86 70917.2 0.4 0.14 11 WYM61 69977.1 0.4 0.07 12 WYM30 69670.2 0.40.10 11 LAB259 69399.6 0.4 L 19 WYM61 69977.4 0.4 0.03 14 WYM30 69670.10.4 0.06 14 LYM91 69394.2 0.3 0.21 8 CONT. — 0.3 — — WYM105 70928.2 0.40.16 11 WYM86 70918.7 0.4 0.08 12 WYM18 70937.11 0.4 0.21 8 CONT. — 0.4— — WYM48 69973.1 0.4 0.04 14 WYM86 70920.4 0.4 0.23 7 WYM48 69973.5 0.40.16 9 WYM32 70416.6 0.4 0.22 7 LYM91 69392.4 0.4 0.01 16 CONT. — 0.4 —— LYM490_H1 71155.4 0.5 0.16 11 CONT. — 0.5 — — WYM35 71163.1 0.5 0.25 8WYM90 71891.2 0.5 0.28 8 CONT. — 0.4 — — WYM112 69928.3 0.5 0.10 13WYM34 71768.2 0.4 0.26 9 WYM34 71769.1 0.5 0.09 13 WYM71 72162.1 0.40.28 8 CONT. — 0.4 — — WYM21 71763.3 0.5 0.30 9 CONT. — 0.5 — — WYM3571162.9 0.5 0.24 9 CONT. — 0.4 — — WYM90 71888.1 0.4 0.26 8 CONT. — 0.4— — WYM79 69537.4 0.4 L 21 WYM70 70034.6 0.3 0.01 12 WYM79 69537.3 0.3 L12 WYM24 69663.3 0.3 L 14 LYM320 69406.3 0.3 0.07 9 WYM79 69537.2 0.3 L12 WYM93 69690.2 0.3 L 11 WYM94 69628.3 0.3 0.06 12 CONT. — 0.3 — —WYM24 69667.7 0.3 0.02 16 WYM79 69536.2 0.3 0.13 7 WYM31 69730.9 0.30.22 6 WYM15 69495.5 0.3 0.10 10 WYM70 70034.2 0.3 L 12 WYM31 69730.70.3 0.02 12 WYM15 69497.4 0.3 0.17 8 CONT. — 0.3 — — WYM94 69631.2 0.30.11 11 WYM31 69730.4 0.3 0.29 5 CONT. — 0.3 — — WYM15 69499.5 0.3 0.099 WYM93 69686.1 0.3 0.15 7 WYM15 69495.2 0.4 L 18 WYM79 69541.2 0.4 L 16WYM55 69509.5 0.3 0.11 8 CONT. — 0.3 — — WYM70 70039.7 0.4 0.06 10 WYM6569520.4 0.3 0.20 8 CONT. — 0.3 — — WYM31 69729.3 0.3 0.29 4 WYM6569519.3 0.3 0.14 5 WYM94 69629.3 0.3 0.07 9 CONT. — 0.3 — — WYM6569523.2 0.3 0.11 8 WYM79 69538.1 0.3 0.13 7 CONT. — 0.3 — — WYM2469662.2 0.4 0.01 12 WYM94 69630.1 0.3 0.13 7 WYM24 69662.1 0.3 0.22 6WYM93 69688.1 0.3 0.02 9 WYM79 69539.4 0.3 0.23 6 CONT. — 0.3 — — WYM5569507.2 0.4 0.28 6 WYM70 70039.6 0.4 0.25 6 WYM22 69504.2 0.4 0.21 7CONT. — 0.3 — — WYM64 72486.1 0.3 0.13 9 WYM85 71526.6 0.3 0.09 10 WYM2971879.3 0.3 0.22 8 CONT. — 0.3 — — WYM20 72492.1 0.3 0.12 10 WYM3871690.2 0.3 0.03 11 WYM64 72485.8 0.3 0.16 8 CONT. — 0.3 — — WYM372477.1 0.4 0.10 10 CONT. — 0.3 — — WYM85 71529.3 0.3 0.29 8 CONT. — 0.3— — WYM38 71690.3 0.3 0.11 13 WYM20 72491.6 0.3 0.20 10 WYM64 72481.70.3 0.04 16 CONT. — 0.3 — — WYM3 72478.3 0.3 0.29 6 CONT. — 0.3 — —WYM64 72485.4 0.3 0.18 8 CONT. — 0.3 — — WYM64 72485.2 0.3 0.18 7 WYM8571526.3 0.3 0.21 7 CONT. — 0.3 — — LYM350 69417.1 0.6 0.18 10 CONT. —0.5 — — WYM43 69949.7 0.4 0.20 14 WYM23 69658.2 0.4 0.14 15 WYM6770023.2 0.5 0.03 24 WYM43 69949.3 0.5 0.04 22 WYM91 70012.7 0.4 0.06 19WYM72 70043.7 0.4 0.10 18 WYM72 70044.1 0.4 0.17 14 WYM43 69944.4 0.50.05 21 WYM43 69949.10 0.4 0.08 19 WYM67 70023.1 0.4 0.17 15 WYM2369657.4 0.4 0.12 16 WYM72 70043.2 0.4 0.22 13 WYM23 69660.3 0.4 0.16 15WYM23 69661.7 0.4 0.21 13 CONT. — 0.4 — — Table 62. “CONT.” - Control;“Ave.” - Average; “% Incr.” = % increment; “p-val.” - p-value, L - p <0.01.

Example 20 Evaluating Transgenic Arabidopsis Under Normal ConditionsUsing In Vitro Assays [Tissue Culture T2 and T1 Plants, TC-T2 and TC-T1Assays]

Surface sterilized seeds were sown in basal media [50% Murashige-Skoogmedium (MS) supplemented with 0.8% plant agar as solidifying agent] inthe presence of Kanamycin (used as a selecting agent). After sowing,plates were transferred for 2-3 days for stratification at 4° C., andthen grown at 25° C. under 12-hour light 12-hour dark daily cycles for 7to 10 days. At this time point, seedlings randomly chosen were carefullytransferred to plates containing ½ MS media (15 mM N). For experimentsperformed in T2 lines, each plate contained 5 seedlings of the sametransgenic event, and 3-4 different plates (replicates) for each event.For each polynucleotide of the invention at least four-five independenttransformation events were analyzed from each construct. For experimentsperformed in T₁ lines, each plate contained 5 seedlings of 5 independenttransgenic events and 3-4 different plates (replicates) were planted. Intotal, for T₁ lines, 20 independent events were evaluated. Plantsexpressing the polynucleotides of the invention were compared to theaverage measurement of the control plants (transformed with an emptyvector containing the selection marker or GUS reporter gene under thecontrol of the same promoter) used in the same experiment.

Digital Imaging—

A laboratory image acquisition system, which consists of a digitalreflex camera (Canon EOS 300D) attached with a 55 mm focal length lens(Canon EF-S series), mounted on a reproduction device (Kaiser RS), whichincludes 4 light units (4×150 Watts light bulb) and located in adarkroom, was used for capturing images of plantlets sawn in agarplates.

The image capturing process was repeated every 3-4 days starting at day1 till day 10 (see for example the images in FIGS. 3A-3F). An imageanalysis system was used, which consists of a personal desktop computer(Intel P4 3.0 GHz processor) and a public domain program—ImageJ 1.39[Java based image processing program which was developed at the U.S.National Institutes of Health and freely available on the internet atHypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/]. Images werecaptured in resolution of 10 Mega Pixels (3888×2592 pixels) and storedin a low compression JPEG (Joint Photographic Experts Group standard)format. Next, analyzed data was saved to text files and processed usingthe JMP statistical analysis software (SAS institute).

Seedling Analysis—

Using the digital analysis seedling data was calculated, including leafarea, root coverage and root length.

The growth rate for the various seedling parameters was calculatedaccording to the following formulas XXI (GR leaf area, below). XXII (GRroot coverage, described below) and XXIII (GR root length, below).Growth rate of leaf area=Regression coefficient of leaf area along timecourse.  Formula XXIGrowth rate of root coverage=Regression coefficient of root coveragealong time course.  Formula XXIIGrowth rate of root length=Regression coefficient of root length alongtime course.  Formula XXIII

At the end of the experiment, plantlets were removed from the media andweighed for the determination of plant fresh weight. Plantlets were thendried for 24 hours at 60° C., and weighed again to measure plant dryweight for later statistical analysis. The fresh and dry weights wereprovided for each Arabidopsis plant. Growth rate was determined bycomparing the leaf area coverage, root coverage and root length, betweeneach couple of sequential photographs, and results were used to resolvethe effect of the gene introduced on plant vigor under optimalconditions. Similarly, the effect of the gene introduced on biomassaccumulation, under optimal conditions, was determined by comparing theplants' fresh and dry weight to that of control plants (containing anempty vector or the GUS reporter gene under the same promoter). Fromevery construct created, 3-5 independent transformation events wereexamined in replicates.

Statistical Analyses—

To identify genes conferring significantly improved plant vigor orenlarged root architecture, the results obtained from the transgenicplants were compared to those obtained from control plants. To identifyoutperforming genes and constructs, results from the independenttransformation events tested were analyzed separately. To evaluate theeffect of a gene event over a control the data was analyzed by Student'st-test and the p value was calculated. Results were consideredsignificant if p≤0.1. The JMP statistics software package is used(Version 5.2.1, SAS Institute Inc., Cary, N.C., USA).

Experimental Results:

Tables 63-65 summarize the observed phenotypes of transgenic plantsexpressing the gene constructs using the TC-T2 Assays.

The genes presented in Table 63 showed a significant improvement as theyproduced larger plant biomass (plant fresh and dry weight) in T2generation when grown under normal growth conditions, compared tocontrol plants. The genes were cloned under the regulation of aconstitutive promoter (At6669. SEQ ID NO:9405).

The evaluation of each gene was carried out by testing the performanceof different number of events. Some of the genes were evaluated in morethan one tissue culture assay. The results obtained in these secondexperiments were significantly positive as well.

TABLE 63 Genes showing improved plant performance at normal growthconditions under regulation of At6669 promoter Gene Dry Weight [mg]Fresh Weight [mg] Name Event # Ave. P-Val. % Incr. Ave. P-Val. % Incr.WYM40 71881.6 6.1 0.22 18 142.5 0.13 33 WYM8 71394.3 6.8 0.05 32 144.10.09 34 WYM8 71398.4 — — — 123.6 0.25 15 WYM36 71030.2 7.2 0.01 38 142.50.02 33 WYM40 71883.5 6.2 0.06 20 129.5 0.05 20 WYM104 70921.1 6.9 L 33142.1 L 32 WYM8 71397.2 6.2 0.12 19 — — — CONT. — 5.2 — — 107.4 — —WYM107 69962.1 8.4 0.17 33 145.1 0.22 26 LYM332 69412.2 8.4 0.02 34149.0 0.05 29 WYM1 69695.2 — — — 123.5 0.26 7 WYM1 69693.2 7.1 0.17 13126.4 0.19 10 LYM332 69412.5 9.0 L 42 171.5 L 49 WYM59 69705.1 9.6 0.0652 170.4 0.07 48 CONT. — 6.3 — — 115.3 — — WYM36 71031.2 5.8 0.10 58119.7 0.07 65 WYM104 70921.8 4.6 0.29 25 112.9 0.16 55 WYM104 70925.25.5 L 51 130.3 0.01 79 WYM104 70925.3 5.5 L 49 101.1 0.06 39 WYM3671033.6 7.1 0.02 92 147.4 L 103 CONT. — 3.7 — — 72.7 — — Table 63.“CONT.” - Control; “Ave.” - Average; “% Incr.” = % increment; “p-val.” -p-value, L - p < 0.01.

The genes presented in Tables 64-65 show a significant improvement inplant performance since they produced a larger leaf biomass (leaf area)and root biomass (root length and root coverage) (Table 64) and a highergrowth rate of leaf area, root coverage and root length (Table 65) whengrown under normal growth conditions, compared to control plants. Plantsproducing larger root biomass have better possibilities to absorb largeramount of nitrogen from soil. Plants producing larger leaf biomass havebetter ability to produce assimilates. The genes were cloned under theregulation of a constitutive promoter (At6669). The evaluation of eachgene was performed by testing the performance of different number ofevents. Some of the genes were evaluated in more than one tissue cultureassay. This second experiment confirmed the significant increment inleaf and root performance. Event with p-value<0.1 was consideredstatistically significant.

Table 64 Genes showing improved plant performance at normal growthconditions under regulation of At6669 promoter Gene Leaf Area [cm²]Roots Coverage [cm²] Roots length [cm] Name Event # Ave. P-Val. % Incr.Ave. P-Val % Incr. Ave. P-Val % Incr. WYM104 70926.1 — — — 9.4 L 35 7.30.07 17 WYM104 70921.5 — — — 7.9 0.19 13 7.0 0.09 12 WYM40 71882.2 — — —— — — 6.7 0.25 7 WYM104 70922.3 — — — — — — 7.3 0.04 17 WYM40 71881.60.6 0.23 14 10.0 0.09 45 7.0 0.17 12 WYM8 71394.3 0.7 L 35 9.0 0.03 307.0 0.02 12 WYM36 71031.2 — — — — — — 6.6 0.20 5 WYM8 71398.4 — — — — —— 6.6 0.20 6 WYM36 71030.2 0.6 L 26 8.3 0.07 19 — — — WYM40 71883.5 0.60.06 13 — — — — — — WYM104 70921.1 0.6 L 23 7.6 0.29 10 — — — WYM871397.2 0.5 0.25 8 — — — — — — WYM8 71395.5 — — — — — — 6.5 0.26 3 WYM4071880.2 — — — — — — 7.4 L 18 CONT. — 0.5 — — 6.9 — — 6.3 — — WYM5969704.11 — — — 5.9 0.09 19 6.5 0.02 19 WYM107 69962.1 0.6 0.14 21 6.50.08 32 5.8 0.20 6 WYM107 69962.3 0.5 0.26 6 — — — — — — WYM107 69962.40.5 0.22 9 6.1 0.05 24 5.8 0.27 6 LYM332 69410.2 — — — 5.8 0.18 19 5.80.22 6 LYM332 69412.2 0.7 L 30 6.7 0.01 37 — — — WYM9 69551.10 — — — — —— 6.1 0.01 12 WYM1 69692.7 — — — — — — 5.8 0.22 5 WYM1 69697.1 — — — 6.10.05 25 6.3 0.02 15 LYM332 69410.3 — — — — — — 5.7 0.10 4 WYM1 69695.10.6 0.11 12 5.5 0.19 11 5.9 0.16 8 WYM1 69695.2 0.5 0.15 9 — — — — — —LYM332 69413.4 — — — — — — 6.2 L 13 WYM1 69693.2 0.7 L 34 6.6 L 35 6.7 L23 WYM76 70028.2 — — — 6.8 0.06 38 5.7 0.28 5 WYM1 69692.6 0.6 0.09 136.0 0.09 23 6.3 L 15 LYM332 69412.3 0.5 0.24 9 — — — 5.7 0.14 4 LYM33269410.6 0.6 0.15 10 5.3 0.17 9 5.8 0.17 6 LYM332 69412.4 0.6 0.16 22 — —— — — — WYM59 69704.6 0.6 0.11 13 5.9 L 20 6.3 L 15 LYM332 69412.5 0.7 L41 7.1 0.02 46 5.8 0.19 6 WYM1 69693.4 — — — — — — 6.1 0.01 12 WYM5969705.1 0.7 0.01 46 7.9 L 61 6.5 L 19 WYM59 69708.2 — — — — — — 5.9 0.178 WYM59 69704.4 — — — — — — 5.9 0.03 9 WYM59 69708.3 — — — 5.8 0.17 195.7 0.27 5 WYM9 69553.6 — — — — — — 6.3 L 16 WYM9 69550.2 — — — — — —5.6 0.22 3 CONT. — 0.5 — — 4.9 — — 5.5 — — WYM36 71031.2 0.5 0.08 53 7.70.10 22 — — — WYM36 71033.4 0.4 0.11 16 — — — — — — WYM104 70921.8 0.50.08 37 9.5 0.10 51 7.7 L 18 WYM104 70925.2 0.6 L 59 9.2 0.02 47 7.00.18 7 WYM104 70925.3 0.5 L 39 8.7 0.02 38 6.8 0.11 5 WYM104 70922.3 — —— — — — 7.3 L 12 WYM36 71033.6 0.7 L 85 8.3 L 32 — — — WYM36 71029.4 0.40.07 10 — — — — — — WYM36 71033.2 0.4 0.21 6 — — — — — — WYM36 71034.40.5 0.14 34 — — — — — — CONT. — 0.4 — — 6.3 — — 6.5 — — Table 64.“CONT.” - Control; “Ave.” - Average; “% Incr.” = % increment; “p-val.” -p-value, L - p < 0.01.

TABLE 65 Genes showing improved plant performance at normal growthconditions under regulation of At6669 promoter GR Of Leaf Area GR OfRoots Coverage GR Of Root Length Gene [cm²/day] [cm²/day] [cm/day] NameEvent # Ave. P-Val. % Incr. Ave. P-Val. % Incr. Ave. P-Val. % Incr.WYM104 70926.1 — — — 1.1 0.04 36 0.7 0.09 20 WYM104 70921.5 — — — — — —0.7 0.23 13 WYM104 70922.3 — — — — — — 0.7 0.21 14 WYM40 71881.6 — — —1.2 0.03 47 0.7 0.29 13 WYM8 71394.3 0.1 0.04 32 1.1 0.08 31 0.7 0.26 12WYM36 71030.2 0.1 0.10 29 1.0 0.28 22 — — — WYM104 70921.1 0.1 0.29 16 —— — — — — WYM40 71880.2 — — — — — — 0.7 0.09 18 CONT. — 0.1 — — 0.8 — —0.6 — — WYM59 69704.11 — — — 0.7 0.18 21 0.5 0.03 27 WYM107 69962.1 0.10.26 22 0.7 0.05 32 — — — WYM107 69962.3 — — — — — — 0.5 0.17 15 WYM10769962.4 — — — 0.7 0.06 27 0.5 0.29 13 LYM332 69410.2 — — — 0.7 0.20 200.5 0.07 22 LYM332 69412.2 0.1 0.11 27 0.8 L 43 0.5 0.18 17 WYM1 69692.7— — — — — — 0.5 0.12 18 WYM1 69697.1 — — — 0.7 0.13 22 — — — WYM169695.1 — — — — — — 0.5 0.06 22 WYM59 69704.14 — — — — — — 0.5 0.23 13LYM332 69413.4 — — — — — — 0.5 0.03 24 WYM1 69693.2 0.1 0.04 35 0.8 L 390.6 L 40 WYM76 70028.2 — — — 0.8 0.02 38 — — — WYM1 69692.6 — — — 0.70.10 24 0.5 L 30 LYM332 69412.3 — — — — — — 0.5 0.28 11 LYM332 69410.6 —— — — — — 0.5 0.26 13 WYM59 69704.6 — — — 0.7 0.16 19 0.5 0.21 14 LYM33269412.5 0.1 L 47 0.8 L 51 0.5 0.03 26 WYM1 69693.4 — — — — — — 0.5 0.1319 WYM59 69705.1 0.1 0.01 47 0.9 L 60 — — — WYM59 69708.2 — — — — — —0.5 0.02 30 WYM59 69704.4 — — — — — — 0.5 0.21 13 WYM59 69708.3 — — —0.7 0.24 18 — — — WYM9 69553.6 — — — — — — 0.5 0.09 20 WYM9 69550.2 — —— — — — 0.5 0.14 16 CONT. — 0.1 — — 0.6 — — 0.4 — — WYM36 71031.2 0.10.01 52 0.9 0.17 21 — — — WYM104 70921.8 0.0 0.03 38 1.2 0.01 51 0.70.05 15 WYM104 70925.2 0.1 L 53 1.1 L 47 — — — WYM104 70925.3 0.1 L 411.1 0.01 40 0.7 0.05 14 WYM104 70922.3 — — — — — — 0.7 0.10 12 WYM3671033.6 0.1 L 83 1.0 0.04 32 0.7 0.19 10 WYM36 71034.4 0.0 0.13 28 — — —— — — CONT. — 0.0 — — 0.8 — — 0.6 — — Table 65. “CONT.” - Control;“Ave.” - Average; “% Incr.” = % increment; “p-val.” - p-value, L - p <0.01.

Results from T1 Plants

Tables 66-68 summarize the observed phenotypes of transgenic plantsexpressing the gene constructs using the TC-T1 Assays.

The genes presented in Tables 66-68 showed a significant improvement inplant biomass and root development since they exhibit increased biomass(dry and fresh weight) (Table 66), produced a larger leaf and rootbiomass (leaf area, root length and root coverage) (Table 67), and ahigher growth rate of leaf area, root coverage and root length (Table68) when grown under normal growth conditions, compared to controlplants. Plants producing larger root biomass have better possibilitiesto absorb larger amount of nitrogen from soil. Plants producing largerleaf biomass has better ability to produce assimilates). The genes werecloned under the regulation of a constitutive promoter (At6669; SEQ IDNO:9405). The evaluation of each gene was performed by testing theperformance of different number of events. Some of the genes wereevaluated in more than one tissue culture assay. This second experimentconfirmed the significant increment in leaf and root performance. Eventwith p-value<0.1 was considered statistically significant.

TABLE 66 Genes showing improved plant performance at norma! growthconditions under regulation of At6669 promoter Gene Dry Weight [mg]Fresh Weight [mg] Name Event # Ave. P-Val. % Incr. Ave. P-Val. % Incr.WYM56 73450 0.0044 0.26 8 — — — CONT. — 0.0041 — — — — — Table 66.“CONT.” - Control; “Ave.” - Average; “% Incr.” = % increment; “p-val.” -p-value, L - p < 0.01.

TABLE 67 Genes showing improved plant performance at normal growthconditions under regulation of At6669 promoter Gene Leaf Area [cm²]Roots Coverage [cm²] Roots length [cm] Name Event # Ave. P-Val. % Incr.Ave. P-Val. % Incr. Ave. P-Val. % Incr. WYM56 73450 0.44 0.1 11 5.920.03 48 5.9 0.007 22 CONT. — 0.39 — — 3.98 — — 4.8 — — Table 67.“CONT.” - Control; “Ave.” - Average; “% Incr.” = % increment; “p-val.” -p-value, L - p < 0.01.

TABLE 68 Genes showing improved plant performance at normal growthconditions under regulation of At6669 promoter GR Of GR Of Leaf AreaRoots Coverage GR Of Root Length [cm²/day] [cm²/day] [cm/day] Event #Ave. P-Val. % Incr. Ave. P-Val. % Incr. Ave. P-Val. % Incr. 73450 0.0460.04 23 0.72 0.01 50 0.67 0.01 25 — 0.038 — — 0.48 — — 0.53 — — Table68. “CONT.” - Control; “Ave.” - Average; “% Incr.” = % increment;“p-val.” - p-value, L - p < 0.01.

Although the invention has been described in conjunction with specificembodiments thereof, it is evident that many alternatives, modificationsand variations will be apparent to those skilled in the art.Accordingly, it is intended to embrace all such alternatives,modifications and variations that fall within the spirit and broad scopeof the appended claims.

All publications, patents and patent applications mentioned in thisspecification are herein incorporated in their entirety by referenceinto the specification, to the same extent as if each individualpublication, patent or patent application was specifically andindividually indicated to be incorporated herein by reference. Inaddition, citation or identification of any reference in thisapplication shall not be construed as an admission that such referenceis available as prior art to the present invention. To the extent thatsection headings are used, they should not be construed as necessarilylimiting.

LENGTHY TABLES The patent contains a lengthy table section. A copy ofthe table is available in electronic form from the USPTO web site(https://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US11242538B2).An electronic copy of the table will also be available from the USPTOupon request and payment of the fee set forth in 37 CFR 1.19(b)(3).

What is claimed is:
 1. A method of increasing yield, growth rate,biomass, vigor, and/or seed yield of a plant, and/or reducing time toflowering and/or to inflorescence emergence of a plant, comprisingtransforming the plant with an exogenous polynucleotide comprising anucleic acid sequence encoding a polypeptide comprising an amino acidsequence as set forth by SEQ ID NO: 246, 6438, 6442 or 6443, or ahomologous polypeptide having at least 95% sequence identity to SEQ IDNO: 246, 6438, 6442 or 6443 and conservative amino acid substitutionswith respect to SEQ ID NO: 246, 6438, 6442 or 6443, respectively whereinsaid exogenous polynucleotide is operably linked to a promoter fordirecting expression of said nucleic acid sequence in the plant, therebyincreasing the yield, growth rate, biomass, vigor, and/or seed yield ofthe plant, and/or reducing the time to flowering and/or to inflorescenceemergence of the plant.
 2. The method of claim 1, wherein said aminoacid sequence is selected from the group consisting of SEQ ID NOs: 246,6438, 6442 and
 6443. 3. The method of claim 1, wherein said promoter isheterologous to said plant cell and/or to said exogenous polynucleotide.4. The method of claim 1, wherein said nucleic acid sequence is selectedfrom the group consisting of SEQ ID NOs: 150, 27, 109, 1447, 1451, 1452and 1453, or a codon-optimized sequence thereof.
 5. The method of claim1, further comprising selecting a plant transformed with said exogenouspolynucleotide for an increased trait selected from the group consistingof: yield, growth rate, biomass, vigor, and seed yield, as compared to anative plant of the same species which is grown under the same growthconditions.
 6. The method of claim 1, further comprising selecting aplant transformed with said exogenous polynucleotide for a decreasedtrait selected from the group consisting of: time to flowering and timeto inflorescence emergence as compared to a native plant of the samespecies which is grown under the same growth conditions.
 7. The methodof claim 1, wherein said promoter is a wheat promoter.
 8. The method ofclaim 7, wherein said promoter comprises the nucleic acid sequenceselected from the group consisting of SEQ ID NOs: 9811, 9806, 9807,9804, 9805, 9812, 9813, 9809, 9810, 9406, 9409, 9407, 9408, 9797, 9418,9799, 9800, 9801, 9808, and
 9803. 9. A method of producing a crop,comprising growing a crop of a plant expressing an exogenouspolynucleotide comprising a nucleic acid sequence encoding a polypeptideas set forth by SEQ ID NO: 246, 6438, 6442 or 6443, or a homologouspolypeptide having at least 95% sequence identity to SEQ ID NO: 246,6438, 6442 or 6443 and conservative amino acid substitutions withrespect to SEQ ID NO: 246, 6438, 6442 or 6443, respectively, whereinsaid plant is derived from a plant selected for increased yield,increased growth rate, increased biomass, increased vigor, increasedseed yield, reduced time to flowering and/or reduced time toinflorescence as compared to a control plant, thereby producing thecrop.
 10. The method of claim 9, wherein said nucleic acid sequence isselected from the group consisting of SEQ ID NOs: 150, 27, 109, 1447,1451, 1452 and 1453, or a codon-optimized sequence thereof.
 11. Anucleic acid construct comprising an isolated polynucleotide comprisinga nucleic acid sequence encoding a polypeptide which comprises an aminoacid sequence as set forth by SEQ ID NO: 246, 6438, 6442 or 6443, or ahomologous polypeptide having at least 95% sequence identity to SEQ IDNO: 246, 6438, 6442 or 6443 and conservative amino acid substitutionswith respect to SEQ ID NO: 246, 6438, 6442 or 6443, respectively, and aheterologous promoter operably linked to said isolated polynucleotidefor directing transcription of said nucleic acid sequence in a hostcell, wherein said amino acid sequence is capable of increasing yield,growth rate, biomass, vigor, seed yield of a plant and/or reducing timeto flowering and/or to inflorescence emergence of a plant.
 12. Thenucleic acid construct of claim 11, wherein said amino acid sequence isselected from the group consisting of SEQ ID NOs: 246, 6438, 6442 and6443.
 13. The nucleic acid construct of claim 11, wherein said nucleicacid sequence is selected from the group consisting of SEQ ID NOs: 150,27, 109, 1447, 1451, 1452 and 1453, or a codon-optimized sequencethereof.
 14. A plant cell transformed with the nucleic acid construct ofclaim
 11. 15. A transgenic plant comprising the nucleic acid constructof claim
 11. 16. A method of growing a crop, the method comprisingseeding seeds and/or planting plantlets of a plant transformed with thenucleic acid construct of claim 11, wherein the plant is derived fromplants selected for at least one trait selected from the groupconsisting of: increased biomass, increased growth rate, increasedvigor, increased yield, reduced time to flowering and reduced time toinflorescence emergence as compared to a non-transformed plant, therebygrowing the crop.
 17. The method of claim 1, wherein said exogenouspolynucleotide encodes the polypeptide set forth by SEQ ID NO:
 246. 18.The method of claim 9, wherein said exogenous polynucleotide encodes thepolypeptide set forth by SEQ ID NO: 246, 6438, 6442 or
 6443. 19. Themethod of claim 9, wherein said exogenous polynucleotide encodes thepolypeptide set forth by SEQ ID NO:
 246. 20. The nucleic acid constructof claim 11, wherein said isolated polynucleotide encodes thepolypeptide set forth by SEQ ID NO:
 246. 21. A plant cell transformedwith the nucleic acid construct of claim
 20. 22. A transgenic plantcomprising the nucleic acid construct of claim 20.